IMHO the issue is just the fact that comm modules kinda suck. Most comm modules are just less cost-efficent than their unit counterparts.
There's basically no module that doesn't suck
take damage modules for instance... they cost 150 metal before morph costs and you get out about 45% of a scorcher... or about 70m of dps...
I know dps isn't everything about a unit but... this is just way too horrible. it's not any better with other comm modules. the shield and area cloak modules are just more expensive than aegis or iris while not being more efficent... would be nice if they were better.
The main reason low level morphs are still efficent is that at least some of the special comm modules are still quite cost-effective. but the majority of the repeatable upgrades just don't do enough
Here's my proposals, going to be a bit conservative I think to not stir balance too much
Damage booster: +15% -> +30% damage
Range booster: +10% -> +15%
Ablative Armor: +750hp -> +1000hp
High Density Plating: +2000hp -> +3000hp
Autoregen: +10hp/s -> +20hp/s
Personal Shield: 1250hp, 16hp/s regen -> 2500hp, 32/s regen
Area Shield: 3600hp, 50/s regen, 12e/s, 350 radius-> 7200hp, 120/s regen, 25e/s, 450 radius
Personal Cloak: Fine as-is
Area Jammer: +60% range, +75% energy use
Area Cloaker: +60% range, +75% energy use
Nanolathe: +4bp -> +5bp, +25 lathe range
IMHO this is still kinda bad, but at least not as bad
Examples of what can be done:
2.5k gets you 8 range modules. this boosts rocket launcher up to 946 range, with 2x120=240 dps. 3 emmisaries cost 2.1k and have 3x86=258 dps and 1150 range. SLAM goes up to 1540 range with 50 dps. Impaler has 1500 range and 80 dps
2.1k gets you 8 damage modules. With machine gun this gets you 1224 dps. the closest comparable unit is... uh... ultimatum. which is squisher but has effectively infinite dps
And for the fun of it all the repeatable upgrades could also go back to maxing out at 8 upgrades
Might make a tweak/mod to test this out with