Perhaps you could do something like using levels or perhaps something more advanced.
"Energy". Energy is earned by staying alive during battle (more on harder difficulties) and upon dying you lose all the acquired energy for that round? Some "weaker" pokemons could then be balanced by having access to evolution trees quicker by using less energy?
I tried your map.
I kinda liked it.
I am not sure I enjoyed the idea of legendaries being playable and rather thought that they would fit as dropped items that can create spells or something along those lines.
Perhaps have them work like the pokeballs from Super Smash Brawl? Or perhaps like the spells from the spell thingy building in Enfos?