You're forgetting the biggest advantage of Super Dominator: money!!! You can scrap each one of those little ships for a few hundred dollars, enough to quick-buy useful ships closer to the front.
My biggest problem with the SAs is that they're unbalanced. Some are incredibly weak:
They give HIVE to the Thalan, but they don't have conventional factories in TA! It should give an efficiency bonus (10% deduction in per-unit cost).
SuperSpy gives one starting spy and a free technology? That's useless. How about decreasing the spy cost? Or making it more difficult to spy on you (takes more turns per spy level, % chance that a "turn" won't be counted, etc)? Or make it easier to spy on someone else (takes fewer turns per spy level, % chance to get an extra "turn")? Or make it less likely to be noticed when you actively spy?
Super Adapter only gets 50% colonization of two worlds. It should be 50% of all, or maybe a new set of 25% techs for all plus reduced research costs for the 50% and 100% techs.
Super Organizer gets all similarly-aligned races flocking to their aid. That's great, except the AI takes a long time to choose an alignment, short of actually giving away XenoEthics. At the least, it should also make it more difficult for similarly-aligned races to declare war on you, or it should work based on "leaning" not only declared alignment.
Super Breeder only works with 100% morale. It should increase breeding rates at lower morale levels, too.
Compared with some which are more well-rounded and complete:
Super Diplomat gets a large diplomacy bonus. Done and done.
Annihilator gets SporeShips technology, and the ability to fully use the worlds they create.
Isolationist limits ship travel in their space, which should be enough. Then they get a bonus 50% barren worlds.
Super Trader gets double trade income, plus all the trade techs - everything you need to focus on trade.
SuperWarrier gets a 100% first-attack. Considering how the game calculates damage, this leads to lots of auto-kills before the enemy gets off a single shot. Makes defense and ship numbers much less useful, so war can be conducted easier.
I really don't get Super Manipulator, I have never played that way.