I played the whole game as loyalist. I finished it and now I am trying the rebel way.
I am pro shaper just because I do not think the rebels are doing the right thing. They are -irresponsibly- sending hordes of monsters and creatures (including the unbound) killing innocent human beings (to me, more valuable than a creation made of essence), burning their crops and destroying their homes. I acknowledge that negotiating pacifically would be very difficult (if not impossible) due to the Shapers' pride. However, they might as well have just fled to some distant island and I don't think the shapers would take the time to chase them all over the world. The free creations could have found a place to live in peace outside terrestria.
I always picture these 2 sides as humans versus robots. What if one day robots decide they are tired of being treated like slaves by the humans and decide they need to kill humans, destroy cities and wage war to make their point, would you also align with them? It's true creations need proper treatment, have dignity(?) and *maybe* they have feelings and I agree Shapers can discuss and analize what they've been doing wrong, but still, life is an unfair place.
(I hope I expressed myself, English is my 2nd language).