Here's a list of things I had planned or wanted in the Tremulous mod I started and abandoned long ago. Some of these might be usable as-is in Unvanquished, but even the ones that aren't might inspire something that could be adapted. Almost all of these ideas I took from some other game (in most cases: Gloom).
Collective alien regeneration - Make the alien regeneration rate based on their proximity to teammates. A solitary alien would have no (or very slow) regeneration, and increasingly fast regeneration for each nearby teammate (up to some limit, say three). The required distance should be small to make it impractical to use in combat (without getting in each other's way). Would promote teamwork and that "part of a swarm" feeling.
Shared radar - Show a radar to all humans near a teammate equipped with a radar. I talked about this a long time ago here. It's basically another opportunity to promote teamwork. Would be best if equipping a radar prevented you from equipping other things, like heavy armor, so that you'd want protection from teammates anyway.
Spiker - An alien structure that instantly fires a blast of projectiles at the first human to enter its (omnidirectional) range. High damage, moderate/slow reload. Fun for aliens because placement would matter a lot more than it does for acid tubes and hives. Fun for humans because they'd actually be dodgeable with skill.
Gasser - An alien structure that periodically spouts a cloud of gas (or acid or whatever) when an enemy is near. The clouds would be affected by gravity, so building them high would make them cover more area. Could fill the same niche that acid tubes do, but would be more interesting for aliens because placement would matter more, and more interesting for humans because the damage isn't constant, so it'd be possible to evade them. Gloom's gasser also obscured human vision.
Invisibility cloak - An ability for aliens to go invisible when not moving and not taking damage. This and the next two ideas I imagined going together on one class (equivalent to Gloom's powerful and stealthy Guardian, but with wallwalking). Cloaked aliens would still show up on radar. Maybe let nearby teammates use the cloak too for some teamwork possibilities (and because it's annoying when teammates ruin your stealth).
Infestation - Alien ability to infest human corpses, turning them into free defensive structures. I could see removing hives but reusing the tracking swarms for infested bodies...
Proximity trap grenades - A supplemental weapon for stealthy aliens. Short range gravity-affected projectiles that would stick to walls and remain in place until a human got near, then explode, slowing and disorienting the human (to make it easier to kill). Should be hard to spot, but destroyed easily with weapons.
Human stealth - Ability for a human to be invisible to alien radar, maybe also with silenced movement and weapon sounds. Should extend to nearby teammates so the stealthy guy doesn't have reason to hate everyone else.
Air cannon - A human weapon that shoots a short-range projectile that does no damage but high knockback, with splash. So you could use it for pushing back aliens, launching teammates (politely!) where they want to be, or "rocket-jumping" without hurting yourself. I actually envisioned this as the secondary firing mode of a shotgun-like weapon for a support class that could use it to help builders get into high places without a jetpack (inspired by the scattergun of Gloom's biotech).
Air jump - A movement ability to jump once in the air. If you're not holding any directional buttons it would send you straight up, otherwise it would be an impulse in the direction you're indicating. I imagine it on a marauder-like class.
Dash - Basically Tremulous's dodge, but not limited to three directions (so a little more like Warsow's dash), and not available to everyone. I imagined it on a human class equipped with a shotgun and painsaw.
Shock grenade - A defensive human grenade that disorients aliens (by instantly randomizing their view). Would have a very short fuse time, so that unless you threw it straight at the ground it probably explode in the air.
Translocator - A movement item for humans. Launch a medium-range gravity-affected projectile then teleport to its location.
Healing pack - A human item to grant health regeneration to the wearer and all nearby teammates.
Pistol - A simple clip-based handgun for humans. Could suitably replace the blaster.
Honorable already-mentioneds:
Flying alien with air lift - In the game I envisioned, builders were far less mobile naturally (no wallwalking, no jetpack) and so to get to high places they had to either stack structures or rely on teammates for help (aliens with a flying class, humans with an air cannon to launch their builder).
Kamikaze - A small, fast, defensively weak alien capable of doing massive explosive damage.
Projectile turret (section 5.2.1.1)