Allow people to turn off Orbitals, either a blanket option, or better still on an individual power basis. Going further you could allow that ability to turn off or limit the numbers of any unit in the game.
Currently the end game in the big AI games (And I think most people playing just AI are doing at least 4 player games and not so much 1v1), because of AI hammering down orbitals you end up with large armies of just Dreadnoughts as everything else just gets fried. Which for me at least is less interesting. I think you could alleviate this a bit, apart from add the orbital jammer, by decoupling the huge quanta boosts the top AI get from their eco boosts, or make it a configurable option as mentioned above.
Not much else to add that I haven't already griped about ad nauseam on the Steam forum. Just wanted to say that I'm glad some people have mentioned it here, too.
Two or three orbital abilities (radiation clouds are several orders of magnitude less annoying than the nukes but still annoying for the same reasons) and the frequency with which they're spammed by the AI are literally the only things keeping me from buying several more copies of the game for my weekly LAN group or recommending the game to anyone else.
Beyond that, a speed-reduction to units retreating-while-firing (at least for the Cronus Dread, specifically) and a fix for the attack-move cursor bug that I reported in the beta would effectively nix all of my major complaints. In my view, RTS replayability is almost wholly dependent on a functional and frustration-free skirmish mode. Clear up the frustrations and continue to add reasonably balanced content and odds are, I'll continue to play and start recommending it to others.