Ok, I thought about things a little more... I'm all for limiting battleships and cruisers, but I don't think limiting mercs to gunboats is going to help matters. Generic pirates, generic military (unless it was removed), police, militaries (which are the ones that make sense), all the pirate NPC factions (even the smallest of them), Zoners... They can ALL load up on cruisers and (if they can afford them) battleships, and independents with these various IDs can still get a battleship or cruiser... But the poor mercenaries can't. This just means that fewer people will play capship whore as a mercenary, they'll just grab a different ID that lets them do it. How does this help matters?
If you're going to start limiting mercs, I think some more balancing needs to be done. Limit generic pirates, the smaller House-specific pirate factions, police, and Zoners to gunboats (I know, Zoners have their own bigger ships, but it doesn't make a lot of sense for there to be many of them). Get rid of the generic military ID (assuming it isn't already). Limit factions to the number of battleships/cruisers they can have, not just how many they can afford.