Shapers are the good guys. Imagine granting freedom to a herd of drooling serviles, allowing them to blindly dabble in magic and genetics. Absolute STATE of Awakened politics. Don't even get me started on "takers".
Serviles aren't exactly human, considering they're a blend of monkey, wolf and octopus. They're nonetheless sentient and skilled enough to build effective societies that can thrive under considerable pressure.
Point is, contrary to a lot of settings where the "talking point" is that no one is the good guy but the end result is that everyone is an asshole instead, Geneforge has an interesting moral quandary:
Shapers are indeed slavers. They're however justified in being
literal creators and in their paternalistic approach: they're nonetheless slavers that often think nothing of erasing a sentient for utility reasons. Most of them are good and care about creation as their children. It adds to the problem that their system while stable
for the moment is shown to be unsustainable long-term: all you need is a bunch of power-hungry Shapers to cause a disaster. Enter canisters and the Geneforge.
Rebels are delusional and they create their own monsters in the Drakons, that are Shapers without morality.
Everything very gray and very questionable. Geneforge is fun, one of the few games where I like to larp as often the rewards and optimization are dogshit (well, using dialogue skills to cheat and doublecross people is larping too).
In G5, siding with the "final solution" dude that keeps creatures in concentration camps is somehow the best ending long-term, though your character, shaper-hitler, and every creation do get completely fucked over.
And siding with Traijkov in GF1 creates a more "equal" society after a devastating war, a society in which you have a premiere role (even if you are ultra-loyal to the Council they'll never trust you completely because canisters). And let's not talk about
Goettsch or the new retard introduced in Mutagen.
Even the Drakon ending, if I remember right, is a "good" one as Ghaldring fails his power bid against you and other Rebels.
Taygen pays an incredibly high price for his plan, and I'm not entirely sure it's worth it compared to pretty much every other ending. It's nonetheless morally gray by design despite, well,
genocide.