i liked the sup com 2 upgrades, it was sup com 2 in general that was disliked i think.
I do feel like the quanta hasn't been fully realized yet.
1. The quanta building needs to be made upgrade-able so you dont have to spam qanta buildings or if they do it is the players choice to do that to spread out his quanta or keep it all in one place.
2. Add more options, like increased vision radius, additional weapon points on units, increased unit speed both movement and turn rate, you could just call it agility upgrade. basically make quanta more of a difficult choice as to where to spend it. Ultimately that depth adds to players finding more weird and wonderful ways for us to do battle. you could even have a quanta upgrade to increase quanta resource gathering! increased metal gathering, increased radioactive gathering. Its almost endless what you could add to the quanta research list.
Making it difficult for the player to decide on whether to spend on research or orbitals would add a lot more depth to larger games.
Also I still think there needs to be more variety in end game units and ultimately larger units above t3 which are extreme in cost but also extreme in firepower and Armour for late game traveling across the map in LARGER maps. The extreme cost would balance this on smaller maps as it would be worth producing verses a t2 spam early. You could call them t4 or experimentals or titans etc ... but make them beefy enough that its worth the massive investment to produce.
Nothing brings players to the table like ridiculously over-sized end game units. Everyone always wants to be the first one to get one out.