Ed, what aspect of S&Bs rules are your players stumbling over? Is it too many details across the board, or is there some particular set of mechanics that's bogging them down? Your answers can help narrow down some recommendations for other d20 sailing ship rulesets.
Essentially, all ship-to-ship rules boil down to sailing, gunnery, crew management and vessel damage. Among the d20 nautical supplements, there are many similarities in all these areas. Some are simpler to run, but sacrifice realism. Others lean toward wargaming strategy at the price of individual character involvement in the battle.
Wooden Ships and Iron Men is a great beer and pretzels wargame, but if your players are finding S&B a little too much, you don't want WSIM.
However, as wargames go, WSIM is pretty abstract. Those who like it, but are yearning for something with a little more realism, should consider the board wargame Close Action. It is very similar to WSIM, but is quite a bit more detailed.
If that still doesn't do it for you, consider going to miniatures rules. Among the best are Heart of Oak, which was produced by FGU in the late 70s as part of their Privateers and Gentlemen rpg. Heart of Oak does one of the best jobs depicting the art of sailing, and is now available again as a pdf. For really top-notch, albeit complicated, gunnery rules, consider Beat to Quarters, a British publication that is sadly out of print. I've long considered merging these two, but it's another project on the backburner.
Carl