Unit caps were the best idea to balance these races out, due to the fact that some ships are overpowered and the only to keep things the way they are is the use unit caps to keep anyone from spaming the most powerful ships in the game.
The Dark Progenitor's ships are overpowered, but this is normal for them, because of this the Dark Progentors are balanced by a strict set of unit caps that are much lower then the other races this is due to the fact that they have the most powerful units in the game and don't need to field very much of them, compaired to the Beast which has high unit caps to balance out their lower technology.
Kardarans, due to their advanced capital ships have a lower capital ship limit, but have a higher fighter and corvette limit, and frigates stay the same. Hiigarans and Vaygr on the other hand, stay the same except for some of their new ships have a limit on them as well.
Now on to the Flagship class.
Flagships aren't motherships like the Vaygr Flagship, no in Dark Wars the Flagship class is a class of ulitmate capital ships that each race can field only one of. Every race has only one Flagship with the exception of the Hiigarans which have 3, but can only have one of them fielded at a time, meaning if the field one of them, they can't field the the other one. The Flagships are:
Commerion, an advanced battlecruiser with advanced armor but not very many weapons,
Omicron, an advanced battleship with lots of weapons but not very much armor.
Sajuuk, The big bad hip we all know and love from the campaign.
The Warlord Dreadnaught, an advanced super capital ship with a mass of missile launchers, laser cannons and plenty of other weapons.
The Redeemer, an super destructive ship that is armed with five frontal Ion cannons, and twelve heavy plasma cannons.
The Dark Star, just like Sajuuk, only with a more powerful phased cannon array, faster engines, and more armor.