I've re-read through both of these rather recently and since both seem to be mostly well-liked, so I'd thought I'd ask which of the two do you prefer?

Think I'd give my vote to the first, at least up to the end of the Land of the Dead arc, since it's not concerned with building a new status quo/continuity it got to do more interesting stories. The main negatives I guess I have against it is it's legs getting cutoff because of Sacrifice /Infinite Crisis and not a fan of some of the art. The main positives I'd give the second run over the first would be better artist game overall, the new continuity building meant he got to do more interesting revamps of most of the villains (Cheetah, Circe, Cale, Dr. Cyber), and even though it ends with stuff unresolved it can be read better as whole run.

Sadly, I just can't pretend they both fit together.