As much as I hate to break the classic doom feel, Doom 3 had former human commandos.
Admittedly they had tentacles and not many plasma rifles (they favoured chainguns), but the name "Commando" would suit things better than "Commander"
Think about it, Through demonic presence an entire base has been mass-corrupted into semi-mindless slaves to evil, Admittedly the commander is supposed to be intellegent but what is he going to lead? Zombies?
Commando suits it better, It signifies independance, efficiency and so on.