If there's no glitch that let's you play Sheik and Zelda at the same time, there will be none for the Pokemon.
The switch move could be lagged. It can also be made so that no jumps or moves can be made after switching in the air. We don't know anything other than what we see on the site.
I'm actually pretty sure this is what's going to happen. The pokemon coming outta the pokeballs are probably going to have some brutal lag, which would mean doing it in the air while recovering is going to send you plummeting. Or, alternatively, if you change in the air the pokemon come outta the pokéball in that "stunned" state from after an airdodge. This one is my personal favorite, because it would allow for some more transformation-mindgaming than the first option.
And now that the "What the HELL?!?!" is wearing off, I'm starting to like the character idea. Think about it. It's a transformation character, ala Zelda. But, unlike Zelda, it
forces you to change every once in a while, so you can't just learn to use one and forget about the others. No, if you want to be a good PT player, you
have to learn to use
all of them,
when to transform, and how to vary your tactics according to the pokémon you're using at the moment. Squirtle is probably fast, but it's sent flying if the opponent so much as coughs strongly on him. Charizard is probably the exact opposite -a Ganon-esque char who, if it hits you, you're in for a world of pain. And the trick to mastering the character is finding a way to balance such opposite styles.
So yes, as a casual who likes tactical characters, I like this idea.
And commend Sakurai for managing to out-mindgame 99% of the Smash community with a single character, of course