TBH, I'm not keen on the new research system. It's more of a "grind" then the previous version, which people found tedious after their 1st-2nd run through. I can't really see how that move the runes around mini game is in any way "fun".
I do like though that research is not a strict tree, you can research direct into the items you are after. No more having to research a ton of stuff just to get my first golem.
I also remember seeing on the MC forums that Azanor wanted to reduce the number of aspects, and now suddenly, we have a ton more then before.
I'm also not that keen on having to babysit the new infusion altar (as impressive as it is) due to the chance of items being destroyed or falling off the pedestals.
I do like that taint is back, I just love having a world eating purple "goo" around the place, although in TC2 it was easy to get out of control.