I love the atmosphere in Xen though - everything feels alien, you get to fight a couple of big boys without conveniently placed stationary guns, and eventually the Vortigaunt bros chill out and stop trying to fry you while the the big baby can't do anything except send you telepathic threats as you close in.
Jumping puzzles might not be the best gameplay but having some kind of break in the action is fitting and its all short enough that it doesn't get too annoying.
The game has a lot of platforming before then. Remember the factory with those conveyor belts? Remember all the crawling through the vents? The game already had a ton of platforming before Xen, but some people seem to have conveniently forgotten about that.
The jumping puzzles in Xen are wierd because everything is supposed to feel alien and that includes the platforming. I'm convinced this is a case of the devs being smarter than the players here. They were trying to make that place feel truly "other" and a lot of people didn't get it.
Compare Xen to the boring as shit Citadel in Half Life 2. Xen is by FAR the more interesting place.