Here are the Pokémon on Naruto's team as per your requests!
Shifter
Species: Male Eevee
Type: *Normal by default, but it changes when he does*
Level: 33
Moves: (Due to genetic tampering and the odd exercises his partner concocts, his moves aren't easy to guess ahead of time. As such this spot is left blank.)
Ability: Whatever suits the situation at the time.
Ibuprofen (Advil)
Species: Male Golduck
Type: Water/Psychic
Level: 29
Moves: Psychic, Psybeam, Confusion, Hydro Pump, Ice Beam, Bubblebeam, Rain Dance, Double Team, Water Gun, Bubble, Reflect
Ability: Swift Swim
Kurama
Species: Male Vulpix
Type: Fire
Level: 23
Moves: Fire Blast, Flamethrower, Ember, Bite, Double Team, Tackle, Smokescreen, Sunny Day, Swift, Flame Wheel, Flame Tackle
Ability: Pick Up
Kiseki
Species: Female Absol
Level: 30
Moves: (Due to the fact she so new, Naruto has no idea about her moves just yet.)
Ability: (He has yet to learn her ability)
As for why there aren't any rare or legendary Pokémon in any of the chapters, that's because it's still rather early. Naruto will eventually encounter a Suicune, Lugia, and Celebi, I can guarantee that much!
Now, on to the story!
Naruto won his next two matches, though on the third one he actually had to call on all three of the Pokémon he was allowed to use. Because this was a ranking exam, he wasn't allowed to evolve Kurama until after the battles were over even though the Vulpix had recently hit level 27.
His only partner from the egg had been awaiting the evolution as much as Naruto, though everyone he mentioned this to agreed that rushing things was a Very. Bad. Idea.
Naruto had read a story of how a Pikachu defeated it's evolved and higher leveled form simply because it used speed against the Raichu. So he put Kurama through the same training Shifter went all those years ago.
Kurama was roughly at the same level Shifter was at that point in time, but he would never be able to match Naruto's first Pokémon partner.
It was a tired team who finally earned the right to challenge a Jounin. If he beat his final opponent, he would earn the Fire Medal easily. He already qualified for the generic one.
His opponent...was Kakashi Hatake. The laziest man Naruto had ever met outside the Nara clan.
Naruto brought out Kurama first. His Vulpix needed more EXP to level up to 30. Kakashi did his usual eye-smile and brought out a Mightyena.
In the end Naruto recalled Kurama before Kakashi hurt him too badly (he was already feeling the effects of two straight battles in a row) and sent out Advil.
Kakashi's first Pokémon was beaten easily, his second, not so much.
It had surprised Naruto to learn that Kakashi had a Jolteon on his team. Even more so when he saw the absurd speed the thing had.
He later learned that it had been given to him by his sensei, and Kakashi had evolved it in honor of the man. Seeing a Pokémon version of the Yellow Flash was something Naruto rather enjoyed.
Watching what happened when he set Shifter on the Jolteon, however, not so much.
The Jolteon, already tired from Advil's Ice Beam, was in a foul mood. It snarled at Shifter like it wanted to shoot a Spike Cannon at him. Naruto didn't like the look at all.
The Jolteon barely listened to Kakashi's commands, often launching attacks without his order. He was almost as bad as Akuma, only this time his opponent actually cared if his partner got set on fire.
Suddenly Shifter went into his new Steel form (which he had yet to use) and on Naruto's command launched an Iron Tail at the Jolteon.
The yellow and white Pokémon got up, but Naruto gulped when he saw the look in his eyes. He had gone from angry to downright pissed. Kakashi actually looked worried about it.
Shifter, on the other hand, looked irritated. This was not how an Eevee was supposed to behave!
So he did something that had Naruto wondering why he didn't think of himself. He bit the Jolteon rather hard on the leg and broke a bone. He didn't notice the spark that went between him and the Electric type. The same spark that went between him and any Eeveelution he encountered for the first time.
Kakashi immediately withdrew his Jolteon (who he named Minato after his teacher) and threw out his last one.
A Houndoom named Jigoku.
Naruto had made a token effort at bringing down Jigoku's HP before he forfeited. He could see easily that Shifter wasn't able to take down the Fire/Dark type, and he didn't see any reason to risk Shifter's health on a mere ranking exam. He would have other chances to get the Fire Medal.
Kakashi applauded his common sense. So did the Hokage and most of the shinobi forces who actually saw their Pokémon as more than pets.
Anko waited in the lounge, taking a deep drink of the ice cold water to soothe her throat. Being the announcer for the final ranking exam was fun, but hell on the throat. It was why Hayate was never allowed to do it, since his lungs were so bad. Finally the Hokage came in with the list of people to earn a Fire Medal, whether it was the standard or the 'True' one.
She enjoyed her ten minute break before grabbing the mike, picked up Seiryuu (her Dragonair. She named it after the God of the East.) and walked out to the stage which was set high enough to avoid getting hit by attacks, and that was before the barrier took effect.
(They had a special barrier to protect the announcer, since sometimes trainers and rangers thought it amusing to aim a few when the announcers annoyed them with sarcastic comments. Sarutobi sometimes said they had to develop it for people like Anko in mind.)
"Sorry for the delay folks! However here are the results! Those who have earned the coveted True Fire Medal are... Gaara no Subaku! Temari no Subaku! Hinata Hyuuga! And... Naruto Uzumaki! The names of those who have earned a standard Fire Medal are...Shino Aburame! Tenten (name cut out by mike)! Rock Lee! And Chouji Akimichi! To all the others, better luck next year!"
The first thing Naruto did once the announcement was made was take all his Pokémon to the Breeders for an all-out physical exam. Followed by a day off just relaxing. Naruto did occasionally pamper his team.
Naruto stared at the man in the hot spring in shock. What the hell did he think he was doing, peeping on the girls like that?! He knew for a fact Kurenai-sensei was on the other side at that moment!
Naruto growled, then leaned down to Shifter.
"Shifter, I want you to turn into your Steel form, sneak up on that guy and bite him as hard as you can in the ass. See if you can do it hard enough to alert the other side," whispered Naruto.
"Vee..." growled Shifter. He liked Kurenai as much as Naruto did.
"!" screamed the pervert, who screamed so loudly that not only did it alert the girls on the other side of the fence, it got the ANBU's attention pretty quick too.
The white haired pervert with the toad was surrounded by ANBU in seconds, and the girls were all grabbing kunai.
One of the ANBU realized what happened, and hid a snicker. Genma may love Jiraiya's work, but even he wasn't stupid enough to piss of Naruto so much that he had his Eevee bite him.
"Jiraiya... Why am I not surprised?" growled Kurenai. She noted it was Naruto who alerted them and nodded at the boy who beamed at her.
"Come on Shifter, let's go swim while these lovely women strangle a pervert!" said Naruto cheerfully.
"Vee!" barked Shifter pleased.
The screams of the pervert was music to Naruto's ears.
Jiraiya was entirely unamused with Naruto when he left the hospital. He was going to be in Konoha for the Chunin exams, and then he was gone. He had actually expected the boy to be there and not take the rankings.
Now Naruto was guaranteed a Chunin Vest once the second half the Chunin exams were over with.
Still, it was fun seeing the look on the kid's face when he had a toad drop on his head. A toad that was easily the size of the average Arcanine. And who reaked to high heaven. At least up until the point that the kid had his bizarre Eevee bite him in the ass again.
"!"
This time the ANBU didn't respond. Jiraiya had chosen to approach the kid on his own free will. If he decided to do something that antagonized the kid's Eevee, then it was his own damn fault.
"Seriously kid, stop setting that freaky Pokémon of yours on me," said Jiraiya, nursing his poor, abused bottom.
"Shifter is not freaky! Keep calling him that and I have him hold you in the air while I tie you to a post!" growled Naruto.
"Eevee can't switch between their evolutionary forms. It's a known fact," he said calmly.
Naruto was ready to shove a kunai where the sun didn't shine.
Instead he had a better idea.
"Call him freaky again and I'll brand you a pedophile," he growled.
"What?!"
"Don't think I won't. NO one insults Shifter or any of my team and lives to get away with it!"
"Get used to it kid. Someone was bound to comment on it eventually. I'm surprised no one has yet," said Jiraiya flatly.
"...Have you even bothered to ask around before you decided to talk to me? Everyone knows why Shifter can change between forms. It's not that big a secret," said Naruto in surprise.
"What?"
"Oi, Old man Teuchi! This dingbat's paying!" yelled Naruto, who vanished. Jiraiya hadn't bothered to count while they were talking (he was too busy trying to ignore the pain he now felt in his ass) but now he did. And he paled.
Naruto and his Pokémon had consumed fifty bowls of the most expensive ramen the stand had to offer. And there was that look in the chef's eye that told him he wasn't going to get out of paying...
Jiraiya's next stop before he went to pester the blond again was his old teacher.
"Shifter? You were dumb enough to insult Shifter to his face?!" said Sarutobi in disbelief.
"I commented on how bizarre that ability was and he threatened to get me branded as a pedophile."
"I don't blame him! Shifter was, as far as we can tell from Hana's extensive tests, experimented on almost immediately out of the egg to change form. I suspect Danzo had a hand in it but never pushed it since no one came to reclaim the Eevee and Naruto didn't want his partner to be hurt any more. It has taken years for Naruto to get Shifter to the point where he can switch without warning, and everyone knows he picked the Eevee off the streets."
"You mean to tell me that an Eevee who can change forms at will is common knowledge?"
"It has been for nearly three years. And no, as far as we can tell it won't be given to his children. When Shifter started getting frisky we let him out with the other Eevee but none of the eggs showed the same trick. He's one of a kind."
Jiraiya pinched the bridge of his nose.
"You mean to tell me my godson found a shiny Eevee and no one thought to tell me?"
Sarutobi laughed, hard.
"You think he's a rare shiny type? Everything about his powers, his attacks, even his speed was all earned the hard way. Shifter and Naruto paid for their power in blood and hard work."
"Yeah, well that bite of that damn Eevee sure as hell didn't feel like an Eevee. It felt more like a damn Feraligatr!" growled Jiraiya.
"That's because Shifter loses teeth every month. He tends to gnaw on toys a lot, and at the moment Naruto has several rock toys for him to chew on. His teeth are very sharp and very strong for an Eevee."
Meanwhile, with Naruto...
"Found it! Finally!" said Naruto. In his hands were a few books on the world before the Cataclysm. (This is what the shinobi called the series of earthquakes that resulted in the landmass changing and the birth of the Elemental Countries.)
"Five thousand ryo for the set," said the clerk bored.
Naruto grabbed several books and brought them to the counter. They were all about Pokémon. Thanks to the fact he had a much, much higher rank than he had before, he only had to pay a fraction of the cost. This was one of the few stores that didn't overcharge him.
Naruto quickly sealed them in a scroll and put it in his kunai pouch. Well, all but one which described the world before the Cataclysm. Kurenai's talk about the world before had gotten him very interested.
And Iruka never covered the days before the Cataclysm. If he had, Naruto might have actually paid attention to his history class.
"In the days of old, before the Elemental countries existed, there were many trainers and Pokémon. It is still unknown how or why, but one day a series of massive earthquakes struck the lands, causing many lands to be reshaped. Islands vanished and new ones appeared (For examples see the Land of Waves in Chapter 5), cities were torn asunder and many people died.
The most astonishing thing was that the Pokémon vanished for ten years, causing many of the humans left behind to learn new skills in order to survive a changing world. This lead to the first appearance of the Shinobi sect and the creation of many villages such as the first Uzushiogakure, or the Village Hidden in the Whirlpools. (For information on Village in the Whirlpools, see chapter 10 about the Hidden Villages)."
Naruto was entranced by the story of how the shinobi first came into being. He spent hours simply reading how the first Uzukage made a bargain with one of the few Pokémon to remain in the world, the Legendary Lugia.
It wasn't until the sun set that he went home.
And it was there he dreamed of a great Pokémon of silver and blue with a cry that sounded so familiar.
A month had passed for the teams, and Naruto was a bit of a celebrity among the trainers.
He had earned more badges than any other genin on one go, some of them so hard to get that most ANBU didn't have them! The end result was that Naruto was getting a lot more respect than he was used to.
Not that he cared, because he finally found one of the places he had been looking for!
A place that sold custom seal balls and a book on how to make your own. Naruto bought a ton of orange, blue, and fire red seal covers and the book. Thanks to his higher rank, the amount of ryo he had to shell out for the covers was roughly the same amount as a D rank mission pay.
He was a very happy boy for the rest of the day.