DPPt had the perfect idea: A partner and Rival each with a different starter. This was also reflected in BW, but removed in B2W2. This I want in XY, to be able to have all three starters in your Pokédex in one game.
I want an important character who isn't an arrogant loser or overly hyper. Cheren was actually pretty cool. But many animes and mangas has all kinds of ideas for us, and Pokémon hasn't seemed to include the "overly timid" person much. A lot of the characters are pretty arrogant and/or childish. Burgundy, Blue/Gary, Ash, etc. What I want is actually someone mature, and someone who won't have a fit if they don't get their way. Again, Cheren was a pretty good example. Silver to an extent, as well, although he sought only to make his Pokémon stronger inconsiderately.
For the past three generations, the fire starters all ended up becoming Fighting-Type. I want something new. In fact, I want some new type combinations, things Pokémon hasn't done before. Water-Fire, Psychic-Ghost, Ice-Steel, the list goes on, because Pokémon keeps reusing types.
I miss Shadow Pokémon. That's all I have to say about this.
GTS limitations. What I mean by that is for GTS to keep impossible requests off the trade list. Too many trolls take up space by showing off their Pokémon and not allowing people to trade for them by asking for Pokémon available only by hacking. This is exactly what needs to stop.