I hate to beat a dead horse, but I think the BSB is better by quite a bit. The BSB has a much better design overall, better sails / flags, a working anchor winch, string rigging, cargo space, a bigger crew, more cannons, a higher piece-count and a full mid-section on the ship.
BB has a better color scheme and the mermaid figurehead is neat, but the rigging is horrible and overly simplified, the mid-section of the ship is plain, the front of the ship has a lot of wasted space, there isn't really any way for the pirates to man the front-positioned muskets because they're too high up off of the deck, the rutter is horribly designed, the ship has no anchor at all, the chain holding up the front sail was a poor choice in my opinion, the railing throughout the ship is somewhat cheap and the entire ship seems flimsy in areas. I am not a fan of how newer Lego sets (especially the BB) require you to pull parts of the set apart to access areas. I don't especially care for how half of the cabin floor is dark grey and the other half is brown either. At least the BSB is consistent. While some of those may be minor gripes, they all still immediately come to mind when I think of the ship, so they were obviously prominent enough to mention them as far as I'm concerned.
I like the old Jolly Roger design much, much more. It wasn't as cartoony. The new figures are better detailed, but again, they're also more cartoony and admittedly, I prefer the '94 - '97 figure design more. Most of this is probably nostalgia, but I sincerely feel like Lego sets more recently have been more about eye-candy and less about actual substance. The typically higher piece count of older sets and less specialized pieces lend better to custom creations as well.
Anyway, I'd probably list the ships like this personally:
BRS
SES (Very close if not equal to the BSB)
RBR
BB
Like others, I tend to think the ships have reduced in quality over time. RBR has a lot of problems as well, but at least it has an extremely memorable design. BB looks like it wants to be the BSB, but it really just seems like a knock-off. It is, however, far more functional as a toy than the BSB or (especially) the SES. This is not to state I think the BB is terrible or anything of the sort-- merely that it could be a lot better when compared to what came before it.
This all coming from someone who has never owned the BRS or SES (I do own the RBR and BB, however), but spending more than my fair-share of time looking at them.
I plan on purchasing a BSB very soon however. Perhaps my opinion will change then, but I very highly doubt it.