Quake 2 does have acceptable, good engaging level design, but it's markedly a step down from the usual idsoft at the time. This is among the first 3D games that placed emphasis on realism and believable consistency, which forces abstract gamey goodness to take a back seat. But it still struck a good balance compared to a lot of games since.
What do I mean?
-Quite a lot of the level design is flat plane, hallways made for places of work, industrial efficiency, productivity.
-With the hub/level continuity design, the desire to be consistent and believable is even more obvious.
-Even for challenges, this rule is rarely broken. Like, there's a quad damage that you get by jumping on crane arms in a manufacturing workshop, and it is all constructed in a way that makes realistic sense. Quake 1/Doom on the other hand would construct the challenge with absolute priority given to the challenge, making no concessions for the believability factor.
-It all blurs into one as a result, with less variety, instead of super memorable levels in Q1 like Ziggurat Vertigo (low g level), Wind tunnels, Door to cthon, The Installation etc.
But still, again they struck an OK balance compared to later games; the levels are still to some degree abstract and gameplay-focused, and there are some memorable bits, but it could have been better. As did the Build Engine games strike a good balance. In fact build engine games were king of mixing reality and game. Along with late 90s Looking Glass style games of course.