+1 to all except for the end-game zone, I'd rather have them work on the new region instead of a temporary end-game zone.
I also see some comments about the "confirm button", and I do agree that it can be frustrating when you accidentally run from it or kill one.
But there seems to be a split of opinion here. What I suggest is the ability to turn this on/off, just like the "defeated gym" message you suggested.
Another problem, in my opinion, is the trading system. When you want to trade Pokémon or buy from the trade house you need an open spot on your team.
I suggest that, when you want to trade a mon or buy from th, it would go directly into your pc if you don't have an open spot and show the current 'error' message only when there's no room in your pc anymore.
This way, when I'm grinding far away from a pokecenter and see an interesting offer on the trade house, I don't have to run all the way back and put a poke in my pc & face the possibility that the offer might be gone.