They're such different games. Wolfenstein gripped me for different reasons, and due to it's pace and variety had me playing it in a more deliberate, careful fasion, and enjoying the environments a lot more. Although you can run and gun there as well (dual assault rifles FTW), the story actually had me sitting up and paying attention, which is a lot more than I could say for the latter part of Shadow Warrior.
I did love Shadow Warrior though. Once you get the hang of the powers and sword, it becomes quite fun. Never had a problem with the difficulty, as soon as a new, tough enemy type showed up, it's just a matter of figuring out a strategy that works, and/or saving the right ammo for it. The only ones that gave me a bit of problem is those guys with the vulnerable part on their back, they were a bit of a pain if you ran out of explosives. Also that demon companion (Shoji was it?) got really annoying after awhile. I know that's supposed to be his shtick, but man it wore out fast. I did like the various environments though.
It really depends what you're in the mood for. I still vote for Wolfenstein though, really satisfying gunplay and very, very polished game overall - graphics, controls, sounds, story, voice over, difficulty curve, boss fights, atmosphere, funny yet serious....etc.