Wow the quality of discussion on this forum is amazing. Just to address a couple of things though with my POV on them.
I agree that would be a one sided approach for most people but I think that is kind of needed as it is a decidedly black and white story for the shapers if you roleplay a realistic personality in Geneforge 3. The argument of the Shapers is primarily that any nastiness is justified by the absolute need to keep shaping and the shaped under control. that The PC of GF3 first experiences the rebellion is of his school being destroyed. Then the PC sees nothing but out of control shaping destroying stuff for the rest of the game until Island 4 - Gull Island. But I'd say island 4 even then the PC meets creations so hostile that the PC would be unconvinced in any case. The only thing the Rebellion really makes as an argument is that Shapers will be defeated and that they offer power. But the first argument doesn't work in an RPG because who would roleplay a defeatist and really a defeatist mindset could not achieve the things the PC is required to. The offer of power doesn't work because for most of the game the Shapers are clearly offering a better deal being the establishment while at the end using canisters will obviously allow the top tier creations, the PC has no way of knowing that or reason to believe it.
I played a rebel in GF3 because the rebels are more fun for me but it isn't a believable character arc. The storyline really only makes sense as a shaper loyalist in GF3. The shaper's are also unpalatable in the game but from a PC point of view it is the only option, it only looks like a decision at all because we are viewing it externally from the lens of having played the other geneforges.
If I was to rewrite it, I would have the school not get nuked but torn apart by competing factions within the student body of loyalists and rebels. Then have the player discover a deserted school when coming back from an expedition or something similar due to civil fighting between the emerging factions. Then Litalia could come and make her pronouncements like the original game. That would help give an unbiased started. Then have more opportunities to see things from the servile side throughout.
For me the rebels always seemed like the realists. That for creations to stand any chance against the shapers it would require extreme measures and that living side by side was essentially impossible because free creations could not co exist with a nation of enslaved creations.
I think one point in the game's favour is that someone can play it and come to the opposite of my interpretation though. That is a sign of good world building.