It has great game mechanics, but in all other manners of design it feels like a hodgepodge of unrelated assets thrown together. Quake 1 had a similar problem early in development, but they managed to tie it together. Quake 3 didn't even bother with a true singleplayer campaign, which seems like a winning move in hindsight, but at the time it was a departure from the norm and I can't help but feel like it was a move they did out of necessity.
While surely being a marvel of software engineering and level design, it had nothing in common with Quake I and II. It is not my intent to be critical here, but QA3 felt like a circus, especially compared with other multiplayer shooters such as the original Unreal Tournament, which had a wonderful mysterious atmosphere to it.
I was just playing something recently and thought "This feels like an Unreal Tournament Space Castle." Can't remember what game it was.
UT99 had some fantastic level design. Facing Worlds, Phobos, HyperBlast, Deck 16, Coret, etc.
Q3 is intentionally stripped down. Primarily due to Carmack's direction. Iirc from his old plan files.