Just revisited Quake 1 and Quake 2 back to back. Quick summary and comparison:
Weapons: Q2. In pretty much every way. Well...with a couple of exceptions.
Challenge: Q1 (AI, level design, resource distribution, everything is somewhat better than Q2).
Level Design: Draw. Q1 levels are perhaps a little more tight, gameplay-centric and enjoyable, but Q2's is still great, and of course got quite ambitious with the hub structure/openness and greater level of detail.
Soundtrack: Q2. Sorry but it's just so fucking badass.
Art Direction: Draw. Q2 is of course more technically impressive, but on a subjective level they're both up my alley.
Which is the better game? Probably Q1 because it's true, the AI in Q2 is flawed. Namely, Beserkers are just pitiful enemies. Iron Maidens far too slow, easy to manipulate, predict and avoid. Same for Tanks. Circlestrafe always remaining behind them and they can't do shit. It's also often far too easy to manipulate AI into meleeing and then just backpeddling, over and over. OTOH you have Icarus, Gladiator and the Gunner which are competent enough enemies. The biggest issue with Q2 I found however was the Power Shield. Did you know there is a hidden difficulty mode in Q2 called "Hard+" that can only be activated via console command? This was how I played the game and it was providing a decent enough challenge early on, but then came the power shield. Even with frequent hyperblaster usage the power shield grants you near invincibility and the game throws plenty of cells at you for it to not ever really run out as long as you don't spam the BFG (which ain't that great anyway. Hyperblaster more than does the job).
Both were a lot of fun and I'd happily still recommend them both, just consider playing Q2 on the hidden "Hard+ Mode" (allegedly quickens enemy attacks times/frequency) because even with that on it gets a bit easy later on. Q1 has slightly more substance (tighter gameplay), but Q2 has slightly more style (namely the weapons and soundtrack, and technical improvements over Q1). Don't listen to the naysayers though. Q2 is in no way a bad game. It's good, even, just not meeting its potential, and a little declined in the solid classic FPS formula, yet it's incredibly easy to overlook these flaws when you look at the state of the modern market. My respect for the design of both games, while not very innovative at all compared to the likes of Duke 3D, shot up a little afterwards. Just so much fun to be had with good old classic combat and level design.
I also replayed Half-Life immediately after...was a little less good than I remember. Lots of nice variety in set pieces, platforming, puzzles etc, but not so enjoyable on replays as you've seen all the (good) set piece splendour before. Combat is also a little boring too. So, so many hitscan enemies. Still way better than HL2 though. And Xen is a perfectly fitting finale. Xen haters can STFU.