These are just some ideas that I, an enormous Mass Effect fan, think would make this mod feel more like you were leading a civilization in the ME universe.

1. Move the unique units to the information era
-That's when ME actually takes place - it doesn't really make sense that civilizations we know most about in their spacefaring stage have most of their special units in the pre-computer age. Their should be a lot more replacers of the XCOM Squad, for example.
2. More focus on Naval units
-A lot of combat in Mass Effect takes place in Space, which is basically just a giant ♥♥♥♥ing ocean made out of vacuum. In practically every sci-fi thing, they refer to space forces as the Navy. Submarines should be turned into frigates, destroyers to cruisers, and missile cruisers to dreadnaughts.
3. Universally available units
-This one's pretty simple - for all ME civilizations, the gunship in the base game should be the A-61 Mantis, the Modern Armor should be the Mako, Hammerhead, Tomkah, or Grizzly (since we don't really know what kind of armor most species have in ME)
4. A counter to the Reaper's Sovereign
-Let's face it, what would Mass Effect be without the Good Commander him/herself? Oh, right, we already saw that. I think it'd be pretty cool if each civilization had their own single starting badass, some similar to a giant death robot, others more like a great general that can actually fight.
5. Make Terminus more like Venice
-Omega is more like a city-state than a civilization; hell, the entire Terminus Systems is just a cluster of city-states. It would make more sense if they started with one powerhouse city and expanded through Great Merchants (or pirates, in the case of Omega) absorbing city-states.