My 2 cents. (Based only on PvE)
1) Sail time - Its just silly to sit, for 2-3 4 real time hours, doing NADA, Maybe an option to speed up time, perhaps at the cost of not being able to fish?
2) Storms - i sailed for 9 Game days to get to a wreck, when i finally got to the general area, a massive storm broke out, visibility was |---| that much (to scale), so i parked my boat, and waited, aaand waited.. 32(!) game days later, i gave up.
3) Wind - STOP SPINNING! uhm, trade winds, ring a bell?
4) Aiming cannons 1 - how can i shoot at a boat that 40% of the time, looks like a submarine. Several times against Trader Cutters and Trander Lynx, only the cabin and abowe is out of the water.
5) Aiming Cannons 2 - if i get to close to a target, and fire, i get 0 hit at all, not hull, sail, like the balls pass right through, doing no damage, but i still see splinters exploding left and right?
6) Aiming Cannons 3 - now this may just be my lack of experience, if so, pardon my noob, but using Long cannons i have a very hard time, getting the distance i think i should. i aim, and fire 1 shot, to check, then fire all, yet they seem to land nowhere near the first shot.
7) Port Access - Some port are almost impossible to enter/exit, due to the VERY narrow channel, and sometimes combined with the wind head on.. Beaufort comes to mind.
8) Tutorial - i started playing recently, and DAMN this game has a VERY steap learning curve. no tutorial, nothing, only a chat, where other players help out most of the time.
9) Servers - i have NEVER heard of any online game, that shuts down all servers, every damn day, for anywhere from 1-2 hours and up to 3-4 hours, now i do understand you do maintanense, on em, updates and such, but surely, this can be done in a better way?
10) Servers 2 - The lack of a EU PvE server. or even an alternate US PvE, Personally i get ping times from mid 90ms to 150ms.
11) Servers 3 - How about Player hosted servers?
12) Bug rapports - When i submit a bug rapport, can i expect some sort of reply on it? if so, how? when?
13) Trading - This REALLY needs an overhaul, its VERY hard, if not impossible, to make a profit large enough to justify the trips (see 1^^)
14) Trading 2 - The Mafia.. i noticed that at most bigger ports, there are sell contracts on all the usefull/hard-to-get stuff, at really insane prices, even sometimes items thats produced in the port, every time an ammount gets released at the low price, a few guys horde it, and jack up prices.
15) Sail time 2 - Can you please disable the 'kicked from server due to being inactive' when the ship is sailing at full speed, would be nice to point ship in the general direction, and be able to do the dishes, while waiting.
better stop now.. sorry for the long post :-)