I had an idea that both factions could unlock different things to do at tech levels 2 and 4. Maybe something like scan from sc2 or maybe summoning a swarm of crabs. Basically something to influence the game in some way.
#Commander abilities
meager pier
tidal seal
I think a system similar to Rising Storm 2: Vietnam or Post Scriptum would fit in this role better. In both of these systems, the commanders have abilities which have very long cooldowns (5-10min) depending on how impactful they are. In RS2, these abilities can only be cast on locations which have been marked by squad leaders, and in PS they can be cast anywhere the commander has vision.
However, I'm not sure that commander abilities fit well into this game. It would be fun for the commanders, but it seems very much like Dram would like to maintain a connection between the units and the commander. The best way to do that is to not allow for abilities likes this, or at least turn them into "non-tangible" abilities (like scouting, econ based, or something that doesn't directly deal damage) that still rely on units/players to be effective.