Actually, a pokemon AoS would be AWESOME.
There are several different themes you could work with.
1) The typical, pick a hero (pokemon), fight it out on lanes, etc.
2) Pick a trainer/hero, who then can choose to learn a variety of moves, based on the pokemon he gets.
3) You could also do a thing where the pokemon trainer is in the background, and you send out different pokemon, all of which share Exp, HP, items, etc, a la SSBB.
Any of those would make players open to trying your map, if only for its originality. Cause honestly, if there's one thing the wc3 mapping community doesn't need, it's another DotA, imo.