There's nothing anyone can do to Supreme Commander and FA to keep it from slowing down, as it's a limitation of its architecture because the majority of its AI, targeting, UI, and general logic was written in LUA. That's the bottleneck. All of that was moved into C++ in SupCom 2, which is why you can have 8 players with 4000 total units with little or no slowdown. (And despite what people seem to believe, Seton's Clutch is the same size in both games.)
People have hacked SupCom 2 to have higher unit caps, and it handles it fine.
Here's 1000 unit cap, 8 players: https://www.youtube.com/watch?v=31_-032hRFs
Adding more players in multiplayer is a networking issue, not a performance one. Each player adds an exponential amount of network traffic, as the peer-to-peer networking sends every player's data to every player. You'd need to switch to client/server to fix that, but then you'd have the issue of server loads and lag, units warping around, etc. And there aren't a lot of games tracking 8000 players simultaneously; games like Planetside 2 aren't necessarily that interested in people outside of a certain radius, whereas an RTS requires precise knowledge of everything on the map at all times (including projectiles, assuming your game is physically simulated like SupCom is instead of deterministic like StarCraft and Age of Empires).
And yeah, making everything a hover unit simplifies animation and pathing, which get crazy expensive as you increase the unit counts. But anyway, there's nothing on the technical side that should keep this game (or any other) from improving the visual quality over SupCom FA or SupCom 2.