We're talking about a game where, in online multiplayer, custom maps and mods don't auto-download, and based on what I've read in the past, Stardock/Ironclad aren't interested in including custom maps as Impulse-downloadable bonus packs, so I would assume they would feel the same way about mods (which don't auto-download either).
If you're getting bored with playing against AI, I suggest trying online multiplayer with Entrenchment. Sins online multiplayer is great fun and offers much more challenging games, human teammates, camraderie, and the chance to make friends and to even use voice comm.
All of that having been said, a capture-the-flag type of mod might be interesting but I'm sure it would require custom maps designed for that kind of game play (wouldn't be a problem finding someone to make them).