Here's what I hope is kept:
The bank, seriously, I remember using this, I didn't have to loose half my money everytime I lost in battles.
The time system, it's arguable that ruby and saphire had one, it didn't use it like these two did, keep that the same way
the days system, really, it was awesome for it to be tuesday in game and tuesday in our time too.
Well, those were my favorite features in GSC, hope they keep them in the remakes.