I want to see the "Schism" in GF4, some shaper on shaper action! and not just the odd encounter, I mean full on multiple shapers in combat with their creations/allies
Civil war where a large break away faction of more enlightened shapers actually want to craft a better world (instead of just being controlled by greedy drakons as in earlier GF), the UR-Drakons could be involved as they evolve into more ethical and enlightened beings. The fact that both sides would end up trampling most of that world into dust would be missed by their arrogant fervour/devotion to their respective ideals.
I would also like to get past this "apprentice" label, surely if you sided with the traditional order of shapers you should be able to become a full shaper (possibly with some improved powers - I favour "command" a spell that allows shapers to strip control of a shaped creature from another shaper and/or rogue shapings - control stays for that area only). The renegades could develop counter powers at higher levels. This would allow very fluid shaper duels where wrestling control of the correct creatures at the right moment would be as important as shaping creatures.
A nice touch would be the reappearance of a strange powerful nemesis who would be a character that had completed GF 1,2 or 3 to oppose the player (would make for a much more equal final opponent)
Larger map with some timeline driven ebb and flow of territory gained lost to give a feeling of urgency but not panic.
The ability to produce serviles/intelligent serviles
Shapers should have more ability to control those immediately around them but be made to suffer the consequences of exerting too much control.
The schism could be over the ethics of creating intelligent self aware creatures and allowing them the rights to make deciscions and lead a life of their own.
GF 3 is too black and white and the rebels are insane, I honestly cannot see why anyone would side with them. It seems a little more tired than GF1 & 2 but I still like it.
Using the geneforge? It could end with the geneforge being used to remake the world or destroyed to maintain the status quo, either way there should be a few things to do after the geneforge (hunt down the nemesis afterwards would be nice).