Dr. Mario I might excuse as a costume swap if not for Fireballs and FLUDD. They don't really work for him.
So, what the hell? 6 character slots isn't the end of the world (5 to preserve the oldies + Daisy for me). Mario IS the company mascot, after all.
Oh yes, and Pichu does NOT work as a Pikachu skin-swap. The fact that he is smaller, with infinitely cuter vocals and taunts, is the whole freaking appeal. Like I said, if roster space is a concern then I'd group him with possible Pokemon Trainer picks.
So Hypershell, since you're pretty much the only other FE head doing this, who would you pick? I'll probably do a four set from them for the laughs anyway though. 
Well, since I'm one of those "sucks to axe anyone" people, I'd probably preserve Marth, Ike, and Roy. Lethe makes four already.
So far as how to handle Lethe (transforming character is a given), I figure the animal form would hit harder, but fly further when struck (since Laguz tire easily when shifted). As for moves......need more time there. Fire Emblem attacks are basically pulled out of a hat, anyway. But I figure a paralyzing roar should be part of her Final Smash.