You don't need full branching plots to make choices matter. There are a lot of ways a game system can support those choices in an evocative way.
Consider just one example- wandering monsters. Who are those jerks who keep attacking you in the forest in game 2?
Well obviously, they're the remnants of whatever faction you anihilated in game 1. Whatever side you took in game 1, they're what's left of the other side.
They're bitter survivors of your rise to power, with no place in the new status quo- and so they've fled to the deep woods, to wage a resistance. You could get a lot of mileage out of this idea for a managable resource outlay:
*Each of the potential factions filling this role would be comparable in art assets- humanoid, standard combat animations, relativly common voice set.
*Distinctions would be great within that set of resources. Their uniforms and race could be different. Their party composition would be distinct, but well within the existing content- elves might have archers and a pet wolf. Magical foes would have a wizard and some conjured bodyguards.
*Minor plot events could mention the diferences. When you're given bounty hunting side missions, these guys get you extra gold. A wounded soldier you meet in a house of healing has a (one line) story to tell about those vicious renegade wizards/elven snipers/dwarvern sabotuers.
*Assuming there are wandering monsters, and regions, the region encounter likelyhood could be tweaked. If you pissed off the dwarves in game 1, you're more likely to cop a dwarf attack in the mountains, in game 2.
*You could toss in a unique npc for each faction, and place them based on game 1 outcomes. Is that young wizard an ally of yours, or the leader of the arcane resistance? Do you meet that dwarf warrior in a friendly training bout, or is he part of one of the late game party battles with the forces of your new opponent?
These represent relatively minor outlays of resources, within the versatility that an rpg has to have, anyway. And this is just one way a new game could be tweaked, to reflect what happened in the games before it.