The major difference I see in the character (not the art style) is that he traded his pointy little ‘evil vizier’ beard and scraggly undercut sideburns for all-over stubble. Even for humans, that sirt of facial-hair change can make your face look very different.
Most of it’s just the art becoming more ‘artful’ and dramatic rather than comic-booky. (Yes, well aware that those were sweeping stereotypes. Y’all know what I mean.)
Well, as far as I know, Professor Foglio is still doing the pencils for Girl Genius. The first example you show was drawn a long time ago–it is copyright 2000–at his style has evolved somewhat since then, as well as having a different inker/colorist. For Dimo in particular, though, I think maybe the art has changed slightly to show that the character has evolved, now that he has taken on more responsibility and is possibly moving towards being a Jaeger General.
They also lost two and a half years in the time freeze. It makes a lot of sense for Agatha to still look the same and others to have subtle differences in appearance. Look how different Gil looks (after 2+ years of being stressed beyond belief).
I actually like his male characters more then the female one’s (besides Agatha that is).
I love the way Dimo looks now, it might just be me but he seems to show more emotion now. I also like how “fluffy” he looks now, more meat on his bones.