Miko's list of possible conflicts and enemies and solutions. In no particular order. (Written in English)
1. Danzo/Root.
Danzo had been under the tutelage of Lord Second. Lord Second himself didn't hate the Uchiha, but after spending the first years of his life locked in death battles with them certainly didn't help. He was well aware of The Uchiha's flaws through Madara, and he passed this onto Danzo. Not to mention the Sharingan on his arm.
Fixes; Remind Danzo the police force was a gift from Lord Second, his Sensei. Help the village, because ultimately that's what he cares about the most. Despite his decades of suspicious deeds, Danzō only ever acted in what he believed were the village's best interests. If she could could convince him keeping the Uchiha around was in the villages best interests, Itachi wouldn't be forced to execute them. The nine-tails was controlled by the Sharingan, she could try and frame him with the Sharingan on his arm. Danzo had tried to assassinate Hurizen before, she could use that to her advantage. An then there was the case of abducted Konoha citizens. Especially orphans. Wouldn't it be funny if she befriended a few orphans and then happen to bring them straight to her father? Or she could send another clan kid to one of their fathers, as not to cast suspicion on herself.
And maybe somehow she could expose root? Go up to her father and say a scary man with a x scar on his chin said something to her?
2. Clan elders.
The council of clan elders was small, as most people didn't make it to the later stages in life. But they were still a problem. In canon, they were the ones who had first suggested the coup, feeling-rightfully, that the Uchiha weren't getting the respect they deserved and were even being discriminated against.
Fixes; Make sure the Uchiha is getting the respect they deserve. Through various events the clan is being recognized and stereotypes are shifting. Plus with all this extra power it satiates their greedy overstuffed butts. By increasing social standing and connecting with the majority of Konoha through fairs and businesses, it is possible to halt the prejudice right in it's tracks.
And well, they were all old anyway. They'd die soon enough.
3. Orochimaru.
For now, he couldn't get into Konoha. He would be spotted right away. If she stayed here he couldn't get her or Sasuke. Plus Itachi could take him on. And he was involved with Danzo. She could try pitting the two against each other or have them incriminate each other.
4. Tobi/Obito/Madara.
Obito was a dumbass, and one of the victims of the curse of hatred. Even if he was freed from Madara's control, he would still be desperate and deranged. Madara just wanted to destroy the Uchiha. And he wouldn't change his mind either.
Fixes; They were basically in the same boat on this as with Orochimaru. He was able to take advantage of existing anger within the clan and Konoha. If she focused on solving other problems like the clan elders and Danzo, he effectively would be neutered, as he would have nothing to manipulate. And again, Itachi could take the fucker.
5. Sharingan/kekkei genkai hunters.
Stay in Konoha. Buddy system.
6. The curse of hatred.
That talk circle at Akira's house helped many Uchiha overcome trauma and the curse. A little bit more of it could go a long way. But she didn't think Obito would be joining anytime soon.
7. Jealously.
Now this was a problem. People in Konoha were already wary of the Uchiha, and their do-gooding may have helped a bit, some (Danzo) were alarmed by their rapid jumps in power and influence.
Fixes; Share that power and influence. This would rub the clan elders the wrong way for sure. But if they spread out it would be like dividing and conquering. They could make even stronger allies (Friends?)with the other clans by including them, thus having a safety net to fall back on. It wouldn't solely be the Uchiha gaining anymore-it would be every significant clan in Konoha.
It would be like that one spider-man movie; 'You mess with one of us you mess with all of us!'
-End list.