Heh... There's a lot of times where I'll board another ship, and the crew are like in the high lv 20's, that can really suck on solo missions.

Thats why you take the crew out with your cannons(grape shot) before you board the navy ship. Its that much easier if you do it that way. No blood is shed(at least pirate blood, that is :D)

I did... Once. I crippled the ship, Used a grapple hook on the grapple "targets" and swung on. The only problem is that the soldiers were lvl 13 + and I suppose you can guess what happened next...

It's not the best system in my opinion. Sometimes, The ship will sink. Other times it will just sit there and stay there until the timer goes down and it won't let you grapple onto it.

ships
 

Alright, if you haven't figured it out yet....the ships that you can board are flagships they have the flag above their name and level. Ships without that flag will just sink.