I've never really played any multiplayer flash games - mostly TD stuff or shooters, so I'll link some of those.
Creeper World 3: Abraxis - Free flash version of the Steam game Creeper World 3: Arc Eternal. Build a base, expand your territory to collect more power. Use power to supply ammunition to your defenses so the creeper doesn't overrun your base. Creeper basically behaves like water. There are some other, older creeper games as well.
Kingdom Rush: Frontiers - Non-mazing tower defense. Pretty standard stuff.
Desert Moon - Wave defense/tower defense. Place your characters (towers) and turn them so their line of sight is where you want it. Kill waves of aliens. Pretty short game, but I thought it was alright.
Gemcraft - There are a lot of these games. They're all tower defense with some minor mazing opportunities. Make and combine gems with various powers, level up based on your performance in each level. Numerous levels, but each one only takes about 3 - 5 minutes to complete. You won't complete one of these in a sitting.
SAS: Zombie Assault 4 - Top-down shooter, multiplayer optional. Command a soldier and survive against hordes of the undead.
I know you said you didn't really enjoy city builders, but consider giving this one a try.
Rebuild - City builder. Start with a handful of survivors and a small, walled in block. Scavenge for food and equipment, convince survivors to join you, expand your territory, and fend off the rotting masses. You could reasonably finish a game of this in an hour or so once you've figured out the mechanics. There's also a second game if you're interested in that.