I like U2 better because the experience is more polished, and pacing is more even.
However U3 is more interesting, more beautiful and less predictable.
This exactly sums up my thoughts on this as well.
The set pieces in U3 are incredible. The entire section with the boats was really, really well done in terms of setting and art, but it also had several fightfights that were really frustrating.
I was glad they didn't repeat U2's lame final boss thing, though.
More games should have no bosses... -nudges the Souls games and their awful bosses-