I virtually never see gun upgrades on any commanders in any game, I'm surprised you consider it so powerful for how underused it is. Maybe I'm not watching the right games or aren't looking high-level enough.
Either way, I still feel like refits would increase the depth here, we'd see a lot more switching overall as a result, which I consider a good thing because it allows more tradeoffs between utility and resource investment compared to now.
Honestly, I've always felt the issue with air is the overall power of ASFs, not the fact that they grow out of control. One air offensive can be the difference between winning and losing.
I always felt like the static air defences (SAMS etc) should be the big air counter, not other air, followed by mobile ground AA.
Personally I would just nerf ASFs across the board and call it a day.
Full disclosure: I'm not a particularly great player. I mostly play with friends in private games, I'm not really into ranked play much, but I do like to watch casts and streams of higher level players, so I at least know a reasonable amount about how higher-level games play out.
I have noticed in the vast majority of matches that ACU upgrades tend to be quite static, that is, most players tend to go down the same path always - engineering suite 2/3, RAS, maybe microwave laser/teleporter for a desperate Cybran assassination, but generally there's not a lot of variety.
I feel that the main reason for this is because certain upgrades like the engineering suite are almost always useful, while gun upgrades and such generally are only useful when directly in combat. Switching upgrades is extremely costly (you're essentially throwing away the old upgrade, and waiting ~1-2 minutes for the new one), so it's usually not worth trying to use anything other than the most ubiquitous upgrades all the time.
I feel that ACUs (and SACUs) could have a lot more depth if there was a "refit" mechanic, which basically worked like this: Once an upgrade has been purchased, it can be purchased again for 20% of the energy cost, no mass, and 20% of the build time. I'm not sure if the health bonus from purchasing upgrades should always apply, even if they are no longer fitted, that may or may not be balanced.
So, for instance, a skilled player that has purchased the engineering suite and a more powerful weapon upgrade on the same arm on their ACU could switch to the weapon upgrade before going into combat, then when combat is over, they could switch back to their engineering suite for the small cost and time investment of a refit. Right now, that isn't really viable to do.
I feel this would add some utility to some of the lesser-used ACU upgrades, and could add more skill and depth to the game. It would also allow more skilled players to gain some advantages when using their ACU on the front lines.