The reason to use all units is for the variety.
The other, more technical reason, is balance. When there is a fixed hard cap on the number of ships, you can balance the different types against each other.
You could rebalance things by adjusting the energy cost of the various units to reflect their utility. If you think building fleets of just Bomber IVs would be too easy a strategy, then increase their E (and perhaps M) cost until they come back in line. Same with Protectors and other highly effective ships.
Obviously, units that generate free energy would still need to remain capped, but there are only a few of those. IMHO, the main reason "More more more" is totally broken is that it removes the cap on Energy Collectors and ZPGs, effectively giving unlimited energy in addition to removing the ship caps.
If you balance Energy to prevent the player from building 1000 Mk IV Bombers, how will you allow things like Golems into the game? "More more more" doesn't require overbuilding ZPGs or ECs to be broken, it just requires unlocking one top tier bonus ship. Try it - Pick a nice super bonus ship or two, and roflstomp the AI on your preferred difficulty.
Right now, each unlock increases the size of your fleet. This encourages people to get ARSs, to capture Fabricators and Factories (how would they work without caps, BTW), and to do download hacking. There are shades of the CSG arguments there, but I think it really does help people actually experience the game.
Rather than capture two or three systems, unlock Mk IV Bombers, and then spam thousands of Mk IV Bombers and dozens of Assault Transports to win the game.
In an Energy-capped game, increasing your fleet size would come with capturing systems (for additional E-generation), not from unlocking new ships, and with the increased E-cost for (e.g.) Bomber IVs, a player with only 2-3 systems would have neither the resources nor the strategic position to win the game.
I think there would still be plenty of reason to get new ship designs to give yourself more strategic options, but I'd probably remove the HaP cost increase for subsequent hacks to compensate for the fact that it no longer increases your fleet size. K-costs overall could probably be reduced, or K made easier to get, for the same reason. Fabs would still work as they always have, but the E/M costs of MkV units would need to be increased to keep them under control.
Right now, with 2-3 systems, you can win on Diff 9. On Diff 7, it's easy. On Diff 10, you want to keep the AIP as low a absolutely possible. If I could just grab a few systems for K and maybe an unlock or two, then spam Bomber IVs and Assault Transports, I could probably win most of my games. Assuming CSGs are off, of course.
- Just tried it on Diff 9. Captured only two systems, one with a Fac IV in it. Unlocked some turrets, stations, and Mk IV Bombers and Assault Transports, and spammed them hard. Win in 2 hours of gametime (+10). Was harder than I expected, though.
If you reduce K costs, it makes is easier to obsolete units, rending low mark units even more meaningless.
If you increase Metal costs, it just takes more time.
I readily admit that this change would require a lot of rebalancing, and that I doubt it's practical for a retrofit. But IMHO, it would be a more natural-feeling space war simulacrum, with less need for metagame balance straightjacketing, which would make it more fun for me.
Yeah, it would basically require rebalancing everything - Tiers, stats, energy, metal, knowledge, unlocks, hacking, and so on. I, personally, don't think it'd be a good idea. I like the fact that AI War makes everything you get relevant throughout the game and every little bit adds up, so it means that every choice matters the entire time. Sometimes getting a bunch of low Mark units is better than getting a few high Mark ones. Sometimes it is a disadvantage. But either way, they're always an option that someone other than an idiot would take.
I'm not saying it can't be done, and done in such a way that is fun. But I'd miss the variety having all the different types of units around, even when they aren't the best tool for the job.