The problem isn't with gunboats, it's with cruisers, cruisers are too weak, but Gunboats are perfectly fine where they are. I flew a Liberty Navy Gunboat for quite a while, and after that a Lane Hacker Gunboat and then an Order Gunboat (Way way back when the Order still used the old "Lunchbox" gunboats) and then a Liberty Rogue Gunboat, all on different characters of course. But I loved each of them.
But yeah, as far as Gunboat vs Cruiser goes, it really depends on the pilot of the gunboat and the pilot of the cruiser, Cruisers can be big scary bricks of doom, or they can be big slow moving targets, depending on the pilot.