First of all, the problem with disappearing flagships after hooks are fired. POTCO seems to be ignoring this major problem that happens to pretty much every flag for as long as I can remember. This problem has been reported some 104813103613 times already, and still POTCO does not fix it.
Also, the level of the enemies on board should equal the level of the flagship. This rarely happens (rarely is an understatement, actually). I find it strange that enemies on board are often 10 lvs below the lv of the ship. I did not board this lv 38 flagship to fight the level 15 ish noobish enemies.... If the flag is that level, then give us enemies suited for us, not lower level players who can't board her yet. A boss would be a nice addition to flagships too. Ships need captains, right?
Again, back to the "give us lv 50 content", there needs to be ships that have more HP and at higher levels. The lv 45+ Juggies almost never appear, and while it has huge firepower, you can easily burn it down. Right now, max fury is so overpowered that you can pretty much burn down every vessel in ~2 seconds. Not fun.
The Queen Anne's Revenge is nice, but her firepower is so weak, its just sad. After firing around 30+ rounds at our Frigate (not even a war one, just the normal one), our frigate only lost 1% health. Fail....