My two cents:
1. There is no record (that I can find) in which a pirate crew took over a Ship of the Line. They might try, but it was usually considered suicide due to the large complement of marines these ships usually carried. For the sake of keeping the game slightly realistic, it would be ridiculous to see a few dozen Ships of the Line floating around on the Caribbean.
2. Have fun being a target. SvS might be interesting when you have a ship the size of Rumrunner's Island, but EVERYONE is going to be gunning for you. Also, if you list your ship as public, good luck with all the noobs tp-ing to your ship.
3. SotL's are not by any means invincible. I was on Sabona for a fleet once, and myself plus two other war frigates managed to take out the fleet's Ship of the Line with relatively small crews. Don't hype them up to be more than they actually are.
4. Balance. If Disney wants to shoot ship combat straight down the toilet, they need to do little more than introduce the SotL. Honestly speaking, what could stand against you if you had a Ship of the Line? A fleet? Possibly, but those are few and far between. The game is already slightly out of whack with Cannon skills, but if you really want to kill ship combat, bring in a bigger ship.