Basic units do have or count kills, so while heroes - capships - take the exp from grav well, units doing the kills (missiles excluded hopefully) should be getting something.
Non-capships in general will still get destroyed. If vetting it up renders that one unit 1.1-1.2 combat effective, it is not terrible.
This is the thing that killed most rts fun - RA2, RA3 or CnC3 had rather impactful bonuses. However those were tied to value of stuff they destroyed, usually 3x-9x their own cost. (RA2 worked like that)
Rapid autoloader is not weak at all, if you want some proper overkill, do use 5 heavy slugs plus 1 autoloader. 40% passive bonus, 90% on top active one. 250 penetration on the gausses.
Repair unit is also not weak, because it has a passive bonus, that applies nonstop even during jumps. 30 or so on top, if on Kol with active armor means that you get much more effective repairs.
Games without unit exp ended up consistently bad. SIns 1 had only heroes gaining exp. Units and heroes gaining would be a novelty imo, but units themselves, depending on how veterancy is achieved and what kind of bonuses theyd get.
You could have even starbases and base structures gain exp based on their function or use /damage in combat.
There is an RTS in the making SCII-like called Zero Space (suposed to release in circa 2 years)- there are heroes like in WC3, combat and movement looks like SCII, units do get vet, just like the hero. It is a different kind of game than yours, but like in SC-2 campaign, each unit type has 2 tiers of upgrades of : 1 or 2 and 3 or 4, fixed for the rest of the game. (SCII campaign had such system - like Bunker - add 150hp (400 to 550 or hp stays, but bunker adds an MG turret, only one 1 or 2 option))
You do have a sort of more customization with capships here via the slots. There are some that result in a visible change like say on titan getting PD, missiles. But stuff like repair, autoloader, and such generic upgrades, you do not get a visual change.
I didnt play that thing, but some of the mechanics (except those 'global' abilities-sounds like a tabletop 'magic' thing per game or turn) but mechanics-wise there are things you could take a look at (that one looks pretty solid tbh) and see if there are things you like there that could perhaps introduce something more unit types reminiscent of RL (granted, this one plays like in an ocean of space with islands moving, while that one is based on static ground)
Im pretty sure I could come up with all sorts of ideas, the new trade mechanic is better because it is based on RL economy, not monetary economy that doesnt produce stuff. But that would take a few days I guess and Id have to be in a mood for it.