Recently I've seen a trend among Large Train users mounting all Gunboat turrets on their ships instead of Transport turrets. Though there's no rules against it and I'm not suggesting there should be, I think it's horribly unbalancing, as it gives a simple trading vessel greater firepower than a fully loaded military Gunboat. Large Trains are fairly tough with a hull multiplier and the best freighter shield already, all weaponry on-board should really be defensive, which Gunboat turrets are definitely not.
A fix I would suggest is downgrading Freighter weapon slots to level 8, thus making it impossible to mount Gunboat level 9 weapons, but unfortunately doing this also affects the Assault Freighters like the Turanic... though maybe that could use a little nerfing anyway, it'll probably be stronger than Gunboats if Mortars get removed.
I mention this as I think it's a pretty big issue, the majority of players on have at least one Large Train character, and it's still very difficult to cruise disrupt them effectively. Successful pirating is practically confined to capships while Trains are this strong :0/