I'd say armor rotters should just get a "takes extra damage" debuff, would make them far more versatile than they currently are since they currently only do much on things with high armor and of course the durability to require lots of shots to take down.
For AP I'd have them react similar to IREs and Polarizers but based on HP, i.e. no Implosion-style infinite scaling, just something that tops out at, say, 10M HP.
Bombers as a counter are kinda boring considering the massive amount of units we have though. Plus few other ships counter stuff that hard (still hating the damage penalty for forts, I'm thinking bombers should instead get some ability like a directed shield that reduces damage dealt to the bomber from a single enemy). And well, IRL bomber is a class of units, not a single one so you've still got a wide variety of bombers (differing in range, payload, maneuverability, stealth, price, etc) instead of just one and a few gimmick versions. And in games there's usually some sort of defense against bombers (interceptors, flak, ...) that must be destroyed by faster escort units before the heavy bombers can safely move in. Against forts and such the bombers not only don't need escorts, they cannot have escorts because the fort will just slaughter those.