Personally, I’d like it if they let you Pokemon have a second charge move to add a bit more variety to each Pokemon. They’d have to add a few more charge moves to some Pokemon, but I think it would be a cool addition. Like, lets say your battling a Rhydon and you throw out a Donphan. You already saw a Stone-edge from the guy, so you’re expecting it to go down fairly easy, but then the Rhydon hits your Donphan with an unexpected Surf attack, making the battle just that much more costly.
It may not seem like the most necessary addition, but I think it could add a bit of a rouge element to gym battles and make them a bit more challenging again, which I do miss in gyms. I would also be really good in PvP if it ever gets implemented.
But if I had to pick one from the list, probably status effects, add a bit more variety to the game, though abilities are a close second.