After Death
You are a Pokemon Master. A ten-year old, plenty of time to acheive more, train more, battle more. Years and years to do as you wish.
But what comes after this "more"? If you die, with no next of kin, that means your Pokemon will be released. The highest power level possible, volatile, deadly Pokemon in the wild?
Your Shedinja, for example. Virtually indestructible to a wide variety of wild Pokemon. It can steal souls souls! through the crack on its back. Even if it didn't, it could destroy the ecosystems! An ultimate predator, an unkillable one, is the largest threat to wild Pokemon yet!
Call me a doomsayer, caller of the apocalypse. Okay then, what about another Pokemon? Let's say, your Sceptile.
Only found normally as Treecko, a master jungle predator, one that has slain great titans such as Kyogre and Groudon, upon the masses of prey? Why be unkillable when you are fast enough to kill anything else? Speed unrivaled, at a level much higher then the fastest wild Ninjask, with incredible moves; the legendary Technical Machines of Earthquake and Dragon Claw on this demon? What wild Pokemon could kill it when Pokemon League Champions couldn't?
Even worse, what if, forbid, a Pokemon of yours was captured? At a single word, your Gyarados could obliterate towns, Chandelure siphon life energy, Tyranitar necessitate redrawing of maps, Gengar be the most efficient silent killer imaginable, Porygon-Z hack into dangerous code, Charizard destroy towns, Sharpedo sink ships!
Your Pokemon, which fought hard and long to stop Team Rocket, Aqua, Magma, whatever, could be used for much more dangerous means and power! Did you not catch Kyogre and Groudon? If Team Aqua or Magma got their hands on them, with they having proven to owning Master Balls, their goal will have succeeded, and even better, a monstrous Swampert whose Surfs are unrivaled, and a deadly Talonflame to use for aerial support! Dialga, Palkia, Giratina, and even Arceus in the hands of Team Galactic!
Why did you catch all of them? Why did you create such deadly monsters? Tame toward you, but what about after death!?