First time I played Geneforge 3 a few years ago, I got a little bit upset at the Guardian model change. They used to look so unique, cool, and strong. Now Guardians look like your average RPG knight instead of the special, clean, strong appearance of the first two games.
The Shaper's model update, I'm indifferent on. Shapers look really cool despite how simple their design was, which I think is an amazing achievement. Then they got changed into a more intricate, detailed, yet still cool design. I can't really pick between the two, and that's a good thing.