Knowledge and energy are scare. Even underpowered ships would get more use if it wasn't for that.
Here's my thoughts. I'm leaving out the ships that have situational niches that I generally wouldn't use with my strategy, as well as the spire ships which I still haven't used much from the following listing. This is just a list ships that are pretty much entirely outclassed by triangles, and their replacement ships that are the MRLS, Space Tank and Bulletproof Fighter. There are ships besides these I think are underpowered and generally never use, but those have niches that aren't really filled by other things.
Autocannon minipods. They're pretty terrible. Candidate for the worst ship in the game.
Raiders are too expensive. They're more expensive and flimsier than fighters per ship cap, they are far weaker than bombers due to blowing up so fast per ship cap. Large resource drain. If you don't care how long the game takes you don't really notice because you just take all the time you need anyway. Good for the AI though because they don't have a resource cost, doubly so from the significant turret bonus which only works against humans. I'd rather have a second set of fighters or a second set of bombers as human against the AI though, whichever way they're getting used. I guess they didn't get any love after the shields -> armor change which is why they were so good (their range was enough to break bomber shields and thus they had no counters) and still worth their resource cost back in late 1.0 and early 2.0.
Planes take too much power. They have a 2x triangle ship cap and are under fighter strength per ship cap (except they're pretty good at taking down AI Eyes), but take three times as much power. That's a huge drain and I would much rather unlock a second set of standard fighters. Again, if you don't care how long the game takes, you don't notice the power and thus resource drain as much. Good for the AI though because they don't have to worry about power. A little pricey in build cost as well, but it's more handleable than raiders. Since their main utility over default ships would be taking down AI Eyes, which is the only time you can't just bring in all your high power stuff to kill EVERYTHING, their high ship cap/swarm thing kind of puts them at odds with that as another mark against them.
Teleport units are hard to use effectively on offense because they won't stay with the group.
Telestations are way too easy to blow up for their cost and ship cap to use on defense against bombers, which they even have a bonus against so they can do more than scratch the paint. They're way too easily popped by anything else.
Teleraiders are also mostly outclassed by fighters, but at least are numerous enough that bombers waste a lot of damage blowing them up before the teleraiders wear the bombers down. Cheapness keeps them at least somewhat effective. I'd still baaarely want a second set of regular fighters even if just for home defense. Barely. For general useage though, a second ship cap of fighters would be far better.
Acid sprayers have fearsome looking multipliers, but in the end up mostly being weak fighters. There are better picks against polycrystal and neutron isn't that ubiquitous.
Raptors are really fast and easy to explode frigates with much worse damage modifiers. The speed usually isn't that big of an advantage to offset having 1/6 the hp of a frigate for humans. It makes them mostly a minor annoyance even when the AI has them.
Microfighters are, well, weak fighters, even with a ship cap of them vs a ship cap of standard fighter. I'd still rather unlock a second set standard fighters because microfighter AP doesn't keep up with bombers, and the ship cap total raw dps isn't anywhere near as high. They probably need to get hit with the same rebalance as standard fighters did as well as putting their AP in line with regular fighters. If they were more like bulletproofs and were Fighters+detectors they would be much higher on the pick list, possibly on par with the MRLS, but not quite to FFB or Space Tank levels, but certainly above bulletproofs. If you want to keep them swarmy, just do half the raw damage of standard fighters, half the hp of standard fighters, half the cost, half the power, and twice the ship cap, but leave the AP at standard fighter levels per mk because bomber killing is job #1 for fighters.
Claws, shredders and cutlasses are too easy to blow up, and too hard to use with high K:D superior firepower fleet blobbing unless you like extended micro sessions. I'd much rather have a second ship cap of standard fighters as a human. For the AI they're ok because they get under force fields and ignore tractor beams, but neither of those are particularly compelling in a ship that can't readily blow up AI Eyes or other similar features for a human player. They also are all a little bit on the pricey side for ships that blow up all the time. Claws in particular suffer from an abysmally low ship cap damage rate. Shredders probably suffer from difficulty skew, being far better on lower difficulties where they can get to their replication point, and far worse on higher difficulties where they blow up all the time. Similar for vampire claws. Their health per mk could probably stand to scale better.
Z Chameleons are entirely and severely outclassed by regular bombers as far as ship cap total power goes. Chameleons probably need to at least be bomber levels of power to be a Bomber+ like bulletproof fighters, where I would at least like them as a third ship cap of bombers(after tanks, which I would take before bombers even). Right now they really only get a bonus against force fields and AI Eyes, but Tanks are already Bombers+Fighters On Top, and Z Elec bombers are better too (but worse than regular bombers). They have less damage, less health, less armor and far worse multipliers than bombers. Cloaking before they fire if they stay still doesn't really make up for any of that, even for the AI. It would be better if they were just full cloaking so they could approach AI Eyes better without triggering the system, and that alone might make me pick them above Space Tanks if they were on par with regular bombers in every other way. They might even end up on my favorite ship list because I really hate AI Eyes.
Z Elec Bombers are also quite outclassed by regular bombers. They may be better individually, but ship cap for ship cap, bombers win easy. Tanks are hands down a far superior pick. The only things Elec Bombers have going for them is that the AI has ship minimums in waves that multiply their effectiveness in AI hands, and they are some form of bomber.
Z Mirrors are decent AI ships but terrible human ships. Why bother getting a ship that has to be blown up in order to damage things when I could instead get a ship that has far more permanence and can blow up many things without being blown up itself? For the AI this is ok because it is a forced attrition, so there is at least some cost to humans going through systems (assuming the human ships will blow up in a shot or two vs the mirror, which may or may not even happen) but as a human ship it is a pretty terrible pick from an overall effectiveness standpoint. They're also pricey for something that should be exploding as often as autobombs to be really useful. If they were dirt cheap to where they could be used as the suicide units they beg to be used as, that would work better.
the bulletproof fighter has 79 armour, 89 shipcap.. perhaps round that too 100 armour/shipcap (or even a higher value of armour, they ARE bullet proof) and alter their performance in other ways (speed, cost).
Bulletproofs are currently on my "potentially used" list mainly because they are standard fighters+. Adding armor to them seems a bit too powerful. A reduction in speed isn't too big a deal unless they go below missile frigates. Extra cost could give them the current Raider problem if there's not a comparable survival increase, and just make it another ship to not pick instead of Tanks, FFBs or MRLS.
the spacetank has lost all of its character, its just a slower and more fragile version of the bomber now it has only 500 armour and 40k HP @ MK I.
When did this happen? In my game today tanks still have as much hp and armor as bombers, more dps, and a bonus against both polycrystal (bombers) and artillery (frigates).
armour ships are ridiculous atm (280k Hp & 3000 armour at MK I, which vs attacks that cannot peirce armour is the equvalent of over a million HP each- they cost 300 crystal.) hyper cost effective!
Only if things shoot them. Bomber multipliers get over the armor amount easily too. They're really mostly AI ships, but they can cover for other ships some because several things like to shoot ultra-heavy armor type for some reason, and thus they act as sort of an MMO paradigm tank.