It might be an idea for a harder difficulty level, but once you've stolen a flag, war, or treasure galleon, there really should be future consequences to that.
Case in point, right now if I "appropriate" a Treasure Galleon for myself, as soon as I get it fully upgraded I've more or less won the game and might as well start over. To compound those issues, so long as I'm not currently an enemy to the Spanish crown, I can sail that "appropriated" Treasure Galleon right back into the port it just left/was arriving to and just so long as I pay a pittance in doubloons to the governor for stealing the time-equivalent of an aircraft carrier, all is right and good in the world.
My idea is this: if you steal a large warship or treasure galleon - undeniably a state asset - you will randomly get engaged by warships of an appropriate type (i.e. not sloops of war) trying to take it back from you. This would include not only the power the ship was stolen from, but others as well (including fellow pirates). They won't try to *sink* you, they will merely attempt to disable and board you as to capture the ship. This might very well make it more attractive simply to *loot* treasure galleons at higher difficulties over simply taking them and making the rest of the game from that point on a cakewalk. It'd also give people a reason to put skillpoints into fencing. =/
Also, while we're on the subject of the "big boys" of P&T - the Spanish Flag Galleon really should have super-buffed hull, sail, and rigging options to make it far more attractive as a straight-on warship. Nerf the cargo down to 45-50, but the FG really should be the bruiser, but right now a Treasure Galleon is still the "best" ship all-around.