Try lowering the graphics settings if possible. It's likely you have them set higher than your system is capable of running.
If you have a 64bit OS, the cheapest and immediate performance upgrade you can do would be a simple RAM upgrade. Ram is still relatively cheap these days, and bumping yourself up to 6 or 8GB if possible will yield a nice boost all around, not just in gaming. Modern OS's like Win7 are pretty RAM hungry, and if you are running a game on top of that, it may starve it out causing your OS to Swap/Page RAM onto your hard drive, which is considerably slower in performance. This is likely part of your problem.
Also, a video card upgrade usually is the single most important/cost effective/noticeable upgrade you can do for gaming. It provides immediate and noticeable results. I recommend checking out Tom's Hardware GPU Hierarchy Chart. They update it usually every month and it gives a general idea where your video card stacks up against what is out today. As they recommend, it's usually not worth upgrading until you jump 2 or more levels on the chart. Then you get the best bang-for-your-buck. I tend to upgrade my video card usually once every other year, sometimes every year (depending on my tax refund, hehe). But, I consider this more frequent than most, so every other year or so you can probably get away with and still playing most games on high/medium-high settings, given there are no other bottlenecks such as RAM or really slow hard drives (5400rpm drives).
http://www.tomshardware.com/reviews/gaming-graphics-card-review,3107-7.html
If your specific card is not listed, just round-about-it, such as 6350 round to 6300 series or there-about to guestimate where your out.
Best Answer
You can't really skip the naval part of Black flags. But you can fast travel. I recon about 60% is naval, as that is the key selling point of the game.