Even though the mutation system is great, it is not exactly a hot-take to say, that the Pandorans could use some more unit diversity. And they could use a new mechanic except "shoot-and-cover".
I would suggest an underground unit that has a proximity trigger. For the sake of this proposal let's call it the "fungus-man", although any appearance and abilities are possible.
The "fungus-man" would change up the game dramatically, cause these hidden units mix up the game experience from the strictly overground units that once discovered all carry a sound echo. The fungus-man unearthens when a PP-unit comes within X-tiles (10?) of its hiding place. The possibilities are numerous:
1. A heavily armoured unit that roots the running soldier in place, unit it is killed. No more senseless dashing around the battlefield, because you might get rooted in an open space at the end of your turn, drawing fire.
2. Another suicide unit that unearthens and, in the next turn runs towards the next operatives to explode in an acid/fire/poison-cloud. Though similar to the worms mechanic, the fungus man spawns within the players turn
and needs to be taken down with what shots are left. The killing is more confusing than with the worms.
3. Really anything, that pops up the ground to ruin your plans.
I think PP would really profit from such a surprise unit that a player can unknowingly trigger during his/her turn. Otherwise there are few surprises, because you monitor the movement of your enemies and can plan ahead accordingly. But only one fungus-man popping up forces you to readjust strategy mid-turn.
Lore-wise this could be integrated without any issues. Some semi-intelligent fungus that developed as part of the changing eco-system (mid-game). Maybe a subterrainian version of the egg pods, or any number of things. You'll figure something out :)
Of course the factions could offer some countermeasures to these ambushers: Sensing them (Desciples of Anu), Scanning them (Synedrion). New Jericho would field a WKII inspired Hedgehog minethrower that would launch 24 small clusterbumbs shaking the ground flushing out underground fungus man. (those would not do a whole lot of damage to overground aliens though. It's a decetion system, not a weapon).
I do realize that this is no small fee, but I hope I could show all the benefits a unit that spawns mid-turn could have on the game. Lore- and gameplay integration should also work.