Sort of a combo of stuff to improve from XY and RS as well, but:
-Contests give out BP or a equivalent currency (Similar to the Pokeathalon) to buy items.
-Gym Leader rematches be 1 on 1 and easier to set up.
-More options for GTS for filters. XY was a good start, but there is still a lot of issues. Or hell, maybe even a option to see the damn moveset and capture location of the Pokemon?
-More options for online play, like stadium backgrounds or even 6-on-6 with lv 100 maximum.
-Berry Pots makes a return. Also VS Seeker, but that is asking too much. We will probably get the upgraded PokéNav.
-Super Training still available in some form and with a easier to read EV counter.
-Enhanced Pokedex for Pokemon that have evolutions (Like HGSS had for Pokemon like Mamoswine, etc).
-Better rewards for Battle Frontier from Scott. Or at least a shop (Which I see happening).
-Upgraded Elite Four rematches like FRLG, HGSS and BW2. Grinding was impossible in the original RSE and XY due to weak Elite Four levels and selection.
-Events like in Emerald for Deoxys and Mew and other Pokemon.
-If they allow customization (Which I see happening), have more options for Male characters.
-Better Rival fights. Brendan/May was a letdown, and Wally was a pretty poor replacement.
-Keep some of the enhancements Emerald had for the Team Aqua/Magma stuff (Like the Magma base, more events, etc), but make it similar to RS where each version had their own team. More events to flesh out the teams better like HGSS would be good as well.
-Move Tuitors.
Honestly, with them using the XY engine they are fixing a lot of issues I had with RSE already, so the end product being a combination of the two is already setting out to be great.