If a base ship was to be used for that purpose (and I agree it's a decent idea), I'd rather see it be the missile frigate. They're currently underwhelming, and that might give them some extra oomph in comparison. Bombers are already the god of the triangle, there's no reason to push them higher.
I'm not sure what to do with armor, personally. I definately believe armor should be applied before the multipliers occur for damage boosts. Armor is so all over the place that keeping track of the mechanic for usage on the field is somewhat difficult at best and in the blob it doesn't matter so much.
I already dislike high ROF ships because of the armor mechanic as is. In general I'd like to see very particular ships be the only ones who get armor (or piercing) and make it particular to a style of the craft to allow for more effecient balancing then it being all over the place. In most circumstances I'd personally assume Hit Points to incorporate 'basic armor' as everything out there would have armor. I don't think it should be as pervasive, so I definately agree with that.
Now, as to the actual mechanic itself. I'm not sure. I dislike logarithmic type functions because I really don't want to be trying to do complex math in my head when I'm trying to determine what's a good raid group vs. what the AI has and... yeah, no. KISS, please. However, I don't necessarily have a 'better idea' then what's there now, just that it really needs to be overhauled.