Yeah, I always felt the puzzles part was a major deterrent, as was the limited amount of weapons for each class, and definitely the inherent backtracking. It was more the lack of quality maps I was thinking about, as only a handful of Hexen maps are really worth the time (Deathkings wasn't wholly satisfying in my opinion, feeling at times too much like a slaughter mapset). Shadows of Cronos gets mentioned a lot, despite having been left incomplete, in no small part due to class imbalance according to the author. However, I would definitely recommend Cyrgoth's Revenge and its follow-up Afterlands as the best two Hexen wads ever made.