Don't see how the Shapers are viewed as overtly evil in the beginning games like others have said early in this thread. To me they always came off as people acclimatized to things being a certain way like people once were with Slavery in the Western world. In the end, though, even though they set up a fucked up situation, they're the least of the evils in the world thanks to their rebel creations going nuts and doing things that are the reason why the Shapers emphasized so much control and discipline over their work.
One could compare their struggle against their creations to Rhodesia giving up white rule to preserve their country, essentially abandoning their cause to save what little of their nation as they could.
With that said it took me very little convincing to side with them. The stupid forced dialogue of babbling nonsense to support their side was annoying, but with the above mention of acclimatization it does fit what you'd expect to be regurgitated towards being you've been raised to look on as not even worthy talking to on your level and have always been condescending towards.
I'd have rather had dialogue that was more like "I don't know what is good or bad about the overall situation, but the creations going nuts playing with gene technology without regard needs to be stopped and we Shapers are the only ones that can stop them". It also helped that I've always played a Agent character and going RP it wasn't my place to get my mind lost thinking so big picture but to shut down imminent dangers before they got too big, hence why I eliminated all opposers to the Shapers in the first and then sanitized the entire world in GF2 given that everyone in that valley (and the people just outside of it) were tainted and the only way of containing the danger was to do something as drastic as that (I did like the touch in both games reacting to my decisions by saying that after both events my characters went on to be shadow assassins sent to deal with other dangerous threats and was so badass most Shapers were scared of them).
I think the setting is actually the best allegory presented in gaming, or really any media, about slavery and other RL matters of oppression. It shows that, yes, the people behind it were shitty to set things up and enforce it, but it doesn't change the fact that slaves are now going crazy with powers they're too simple minded to wield respectfully, which again, is a strike against theirs masters for for not educating them well enough and leaving them go wild without a strong hand around.
One could compare it to decolonization in Africa if the colonial powers had left behind modern conventional and nuclear weaponry which the ignorant African countries would then start turning on each other (and themselves) without a second thought. Just look at what's been done on that continent with only AKs and machetes since then.
If presented with that, what is then worse? Re-establishing the old European colonial order and all its known evils or having Africa potentially destabilize the entire world in an indefinite Third World War? I know where I'd stand.
There's Shaper, the class, and then there's Shapers, the organization
How'd he miss this one the character creation?
It clearly described there that Shapers are wizard-scientists that their orders centered around, Guardians are their soldiers and open enforcers while Agents do covert stuff cracking down on opposition in more subtle ways.