If I can summarise what I understand thus far:
Etherjets have uses due to their tractor beams, good dps coupled with very powerful
and useful damage bonuses along with cloaking which complements both the tractor beam and the damage if handled well.
Autocannon Minipods are useful in the game not so much as a bonus ship for the player to use, but as an AI bonus ship to fight against. Kind of a shame, but fair enough.
Space Planes are useful and powerful for knocking out specific targets and then retreating at high speed before they get overwhelmed.
Anti Armor I never really had an issue with over the longer game, so much as why I would want it as a starting bonus ship, but in any case; it's got long range, very high firepower and essentially ignores armour, which makes it very powerful, but it's also hideously fragile.
Tachyon Microfighters have a higher cap health than a fighter cap which could make them a useful "meat shield" or fodder for a black widow's paralysing tractor beams, but come at almost twice the total cost of a fighter cap, so, uh, maybe not?
Laser Gatlings have nothing going for them either at present?
A swarmer AI could also be fun. Maybe we could recommend it for the next expansion, shame that it'd probably fall under the category of an "Easy" AI...