I wish there was more I can do with the game when I'm not out and about. I know the point of the game is to go out and catch Pokemon, but I wish there was a more I can do with the Pokemon after I've caught them. Right now you can only transfer them, power them up, or evolve them. I'd like more things I can tinker with when I'm just sitting at my desk at work.
I also hope there are some "event" style scenarios like maybe a rare Pokemon shows up for a limited time in specific locations. Or a Pokemon trainer pops up randomly and whoever beats him gets a cool reward.