3D would make Sonny lose it's unique, gloomy art style.
Bigger map
I believe that Sonny 2 is the biggest flash game you can make. Isn't there a size limit? Or am I just babbling...
What would be nice is some sort of tying the plot together. I've spent an unhealthily long time sifting through MacGuffins and ambiguous cutscenes to try to discern the plot... to no avail. : (
Maybe some sort of ATB battle system, a la Final Fantasy VII? Of course, there could be an alternate, more traditional system.
Of course, moar items, moar skills, moar levels, moar allies, cooler enemy design, tricker bosses, and better voice acting. Not asking for too much, then...