The frigates have a bonus vs ultraheavy (starbases), and starbases have a bonus against heavy (cruisers). It's a quadrangle, rather than a triangle 
Oh huh...still, I think the cruisers hp is mite too high compared to other ships...
The cruisers also cost a
lot more for the bases spawning them, and only spawn from the large bases in the group spawns.
Basically, they're MkV ships balanced like they had a cap of 4, frigates are MkII balanced like they had a cap of 12, and heavy frigates are MkIV balaned like they had a cap of 12. So a cruiser costs (5/4) / (2/12) = 7.5 as much as a frigate. I think the actual cost number may be higher than that.
One thing the cruisers do is give the champion an obvious place in the outside-base-range fights: stack enough anti-heavy and down those cruisers go. Of course there are other things you could stack instead (anti-medium is good for protecting your frigates from the enemy heavy frigates, since your frigates are what usually get the job done against starbases; or if you have enough anti-ultraheavy you can take the bases yourself).
I just seriously don't like how the spawn rate got incresed the more starbases you destroy...it just feels like rubberband AI in racing games...
I tried it without any adjustment initially and the scenarios just dragged out, so both sides' large bases (not the small ones) produce faster as small bases go down. If you want a lore explanation, its that the large bases are using whatever mineral deposits the small bases were using. Originally I'd designed the scenarios to have little miner ships running around to resources and there's the usual "crash the peon line" tactics, but in the end it seemed overly complicated and more likely to create negative emergent results instead of fun battles.
FWIW, when an enemy small base goes down, your large base gets
more of a boost than the enemy base. Similarly, if your base goes down, the enemy gets more of a boost than you do.
To an extent it actually encourages the snowballing because I found that made for more interesting and less-draggy scenarios, but the underdogs would still have a chance to pull out ahead.
The other thing that comes into play is that both sides scale up (the enemies faster than the allies) with your highest unlocked champion hull size, the number of player champions, and (much less so) with the number of scenarios you've won that game.
So when you're bigger you have to fill bigger things on your feet; otherwise the scenarios would just get easier and easier as the game went on, or I'd have to make them mostly linear in order so they could be balanced against exactly one hull size, etc.
Then again, it's all my opinion...
And player opinions are quite valuable in figuring out how to refine things like this. But they're more valuable when the players have more info about what's actually going on. There's a degree of "black box" to the game by design because it's often more fun to play without knowing all the details, but when time comes to figure out how to make it better, the details need to come out. Hence the above. Albeit I'm rambling because its late and I'm tired
