Fighting/Flying: Serves as team fighting type damage and anti-fighter due to taking neutral from rock and resisting fighting.
Ghost/Fighting: Near perfect Stab. Also shuts down many potent threats like Terrakion.
Ghost/Steel: Incredible defense combo.
Bug/Water: Has potential but is currently limited to Surskit who isn't fully evolved. I could see it on a moon themed bug that is an antithesis to Volcarona.
Fire/Water: Something that works in rain or shine.
Fire/Grass: With chlorophyll and fire STAB it would be perfect for sun.
Better designed starters: I personally found the gen 5 starters to be lackluster compared to previous gens. And for god's sake not another fire/fighting starter.
Skarmory Evo: Gligar got one (granted it was pretty desprate for one) so why not Skarm?
Galvantula Evo: Bug/Electric has potential if they were to increase special attack to at least 100 and add some more to it's durability it would be awesome.
Less event legendaries: Speaks for itself for those who have limited access to them or want to start a new game.
Heracross and Pinsir Evo: Pinsir really got shafted, he really needs an evo to boost him up. Heracross could also use one if it would make him faster. I still dream they get evos that make them look like Kamen Riders.
Less baby pokemon: They rarely add much to existing pokemon (with some exceptions like wobbufett) and they take up space that could be used for something useful.
Keep up the good writing: Gen 5 had great story telling and characters I would like to see similar engaging quality for gen 6
Less HM puzzles: Okay they cut down on HMs but I still find it annoying to carry HM slaves or having to run back to a PC because I don't have the right move. I would love it if you just needed the HM in your bag and one compatible pokemon and you can use the move on the map without teaching it to anyone.
Keep the move tutors: My biggest gripe about the original black and white is that most of my fav moves were gone and it was a pain to breed for them.
A better device: I personally found the C-gear to be less exciting and useful as the pokegear or the poketch. The buff to the Xtranciever was nice though.