I'm still more of a fan of each player messaging me and holding to that choice. I think it removes all bias and doesn't take up that much time. It also doesn't have to rely on an honor system, as I'm the only one that knows the answers.

On the matter of battle switching, it will always need a penalty in my opinion. You're gaining an advantage by switching out and need to take a disadvantage elsewhere. I'm sticking to the rule that a Pokémon will get a free action against you if you attempt to switch out on a Pokémon that has not fainted. Or, they also get a free switch. That's how it works in the games and I think it works here as well. Just so long as people don't infinitely switch for type advantage. In trainer battles against me, I will have a set Pokémon to go out first or next and players will state who they're using before I reveal my choice. This removes all possible player bias. 

OR we could just say no penalties for switching, and everyone agrees not to lolspam switch. That being said, opposing trainers would have as much free reign as you do to switch.