While people tend to focus on the mapping and the stripped-down Quake gameplay, I think there are some subtle innovations that Sauerbraten did that are unrecognized. For example, the announcer loudly notifying you when a major powerup is about to drop. It was always silly that, in old twitch-FPS arena games, the gameplay was heavily based around memorizing the spawn locations and times of the major pickups... Sauerbraten/Cube2 made that informal thing formal by including it in in-game announcements.
And the on-screen text... back then, games were resistent to just sticking the user's name over the player model and uglying up their game. Now, of course, nobody would dream of putting the art over the multiplayer experience like that. Cute related features are how chat text similarly appears over the speaker's head. Also, on-screen numerical damage. Little things that many FPS games of the time insisted on not doing because of "immersion", but MMOs had proven that informative, clear gameplay was more important than immersion.