Tis very easy...
Just make Homeworld 3 with combat like in Nexus, player avatar, rpg elements and FPS shooting ;p 
Have you tried EVE Online? I think that pretty much fits the bill (not that I've played Nexus, or EVE Online for that matter).
For an RTS, the speed, gameplay, and stability (not to mention balance and dynamicness that no other game has managed to pull off) of Starcraft (except for the hovering "planes" - having dynamic planes like in SupCom is more fun to watch, though it makes gunships broken because they don't need to come around for another pass) combined with the scope of Supreme Commander: Forged Alliance, and the depth of the unit abilities and combined arms tactics of Command and Conquer 3 and CNC Generals (artillery beacons/spotters, garrisoning infantry in buildings or bunkers that your riflemen can build on the fly, or being able to upgrade heavy tanks like Overlords to carry infantry).
Other inclusions:
Squad mechanics and customizability (except for maybe the "reinforcing on the fly" - click the "retreat" button to have them return to the nearest barracks or something and they auto-reinforce without needing micromanagement, kind of like in Company of Heroes) of Dawn of War (squad leaders giving abilities or squad bonuses, wargear, special/heavy weapons).
Multiple units can build various things. Engineers can build everything, but some units, like riflemen (if you choose the Allied Infantry doctrine from Company of Heroes, or the GDI riflemen in CNC 3 can build bunkers the can garrison) have limited defensive building options that they can construct on-the-fly to give huge amounts of flexibility.
Faction specific powers from structures (like in CNC 3) plus "General" or "Doctrinal" powers like from Company of Heroes (gained from leveling up) and then
Multiple diverse subfactions of each major faction army (like in the CNC Generals or CNC3 expansions - hopefully with more variety from the base faction like in Zero Hour, the Kane's Wrath subfactions are all pretty similar to the main faction with just extremely minor differences). Say 3 doctrines per faction (potentially per sub-faction) to choose from in-game, and then 3 or 4 main factions and 3 sub-factions per main faction, for a pretty epic amount of diversity in how you can choose to play.
Maybe some customizability for vehicles as well, but as far as I've seen customizability (full customizability, that is, like in the Earth series) tends to detract from the flavor because you can stick *this* weapon on anything without having to really deal with any drawbacks aside from maybe a higher cost. That is, unless they went into super customizability (chassis weight limit, is the weapon turreted, levels of armor plating, size/efficiency/speed of engine, etc.) which would, I think, really detract from a fast paced multiplayer game.
Edit: I'd probably also keep SupCom2's distinction between Minor/Major experimentals (though they'd be Massive and Supermassive classes in my game, I guess), and maybe some kind of modular research capacity like in SupCom2 as well, though that may clash with the General's Upgrades/Powers part of things and I think would throw the game way over the top for complexity/balance.
