I still think they should do like HGSS. Make 2 seperate versions.
Make the plot like emerald, but with a few changes (like the version mascot going to the cave of origin).
Add some more pokemon, keep the exclusives (or just make some pokemon extremely hard to find in one game).
Personally i think that along with some like gallade and roserade, the eevee line, abomasnow, magmortar and electivire line should be added. More gym variation.
I also think juan should have is team redone to Kingdra, Gorebyss, Huntail, Lanturn, Relicanth (all diving pokemon, used dive to get there).