Force Field Bearers - Current godship. Overlapping forcefields and an MRS means never losing ships except to ion cannons. Haven't used since the recent health change, but I imagine they are still #1. Only counter to autobombs, so if you don't take these and the AI gets autobombs, it is like moving the difficulty up by 1. These should really just be a regular default start ship, but cost a lot more knowledge (like 3000 mk1/6000 mk2/9000 mk3, they're that good and I would still do it right now at times) and start entirely locked since they are so unique, so irreplaceable, and so necessary to counter specific units.
Wait, how do FFB help with autobombs? I'm currently playing my first game vs level 7 AIs, and I have FFB and they have autobombs. My FFB don't seem to help at all. The autobombs just go under my forcefields and blowup, causing lots of damage. Granted I was trying to capture a Mark IV planet with only mark II fighters/bombers and Mark 1 of everything else (and actually managed to take it too, just took a few tries. Diff 7 is turning out to be way tougher than the Diff 5 game I just beat), but even when I invaded a Mark 1 planet later the autobombs still hurt me quite a lot when I had FFB. (Just to clarify, the unit you are calling FFB are the same as the unit called Shield Bearers now, right?)
Anyways, other than that I haven't had enough time due to college to play many games, here a some ideas on the few units I have played around with:
Spire Blade spawners: I like them. The blades travel quite far on a planet so they can take out lone units easily instead of having your fleet chase after them, unless said unit is blade immune. The only thing I don't like about them is how the spawned blades make an explosion sound when they die. After taking a planet, if it has a capturable, the spawners will keep spawning blades since there is technically an "enemy unit", so you have to deal with constant explosions till either you kill it, or capture it. Very annoying.
Spire Maws: Interesting unit. I mostly like them, but they take a very long time to "eat" the units. Possibly consider increasing the speed they damage "eaten" units some.
Sintenal Frigates: Very annoying in the hands of the AI. In players hands they can be helpful, taking out far away units.
Zienith Viral shreders: Besides lagging my laptop, which is the only computer I have right now, I mostly like them. They gain numbers rather quickly, but with quite a lot of blade immune ships, don't seem overpowered. The only time they feel overpowered is when a player uses a parasite ship to get a few. Just 2-3 of them become 100s in seconds, even Mark IVs. Consider making them impossible to reclaim. It seems more "fair" to have all those ships if you started with one or got them from ARS, but with the way leech starships are you can just get a whole shipcap from the AI. I personally think Leeching should never get you shipcap of ships you don't "own", just a small amount you can use. Which is why I suggested the limitation of 10% (or some other low percent) shipcap on the parasite topic.
Chameleons: Interesting Idea, but very hard to find use for. Ambushing looks to be a good use for them, so give them bonuses against the types of things you can ambush. That or give them higher attack, but not very survivable. So they ambush, but die rather quickly if the ambush didn't work right (like trying to ambush too many units, or too strong of a unit.) These are the ones I've used the least, so I might be giving an inaccurate account of their balance.
Final Note: Not sure if it matters, but my playstyle is to take most of the ARS (A least 3, usually 4 or all 5), and always get an advanced factory. I also like building many spirecraft and capturing at least 1 golem. Basically I love messing around with lots of interesting units, so that type of playstyle could be affecting how I view ships effectiveness. I never try to compare the bonus ships to the triangle ships either, cause I feel there is a reason you give us the triangle ships every game and not the bonus ones. Triangle ships are supposed to be general-effectiveness type ships, while bonus ships should feel unique in use, at least that's how I feel.