Wow, there's an awful lot of hardcore balance enthusiasts in here. Stamina and switching was a step in the right direction, just not done right:
Stamina is how the PP system transitioned into Smash- after a while, the only move you can use is Struggle. For Smash, it came down to making everything weaker. The system can be changed into something more fair, but whatever it is still has to encourage switching to a new, healthy Pokemon. You are playing with 3 Pokemon, not selecting your favorite and just that one.
Switching's lag is a double edged tactic to switch to a healthier Pokemon, yet not have 3 fighters at your instant disposal. If switching out had no open spots, if you could move at the same moment you could throw up your shield, it wouldn't be so despicable.
Yet it needs to transition from the Pokemon games better. If you switched Pokemon mid fight, your opponent gets a free hit, or they could switch out too. In a non-turn based game, Trainer is the only one switching out. It doesnt need to disappear or become exactly what we want, it's only needs to IMPROVE itself.