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Please forgive me if I missed this. What rough time frame do you mean when you say "winter 2013?"
As JLevine's post intimates- "Winter": can be a major factor in your choices.
During the months of August>November, Roatan sees occasional effects from Tropical Storms (and occasional Hurricanes) that track past to the North. This can cause very sporadic issues in sea & wind conditions along that North coast as well as West End. November is the month that is the rainiest of all in the Bay Islands, no matter which side of the island you might be. During this Caribbean Tropical Storm season, the Bay Islands are about as out of the picture as the ABC islands are... pretty safe.
During the actual Winter months (Dec thru Feb), another weather factor comes into play, locally known as a "Norther". These are (relative) "cold fronts" that descend from... you guessed it, the North. Any kind of sinking weather system from Texas to Louisiana can cause this, but be sure that if a freeze line pushes Southward into Texas>Arknasas, this is going to push down and cause major bad weather in points South: Cancun, Cozumel, Belize and the Bay Islands. The Northern coast and West End will be come untenable for sport diving operations.
AKR, CTD, and Subway have the infrastructure and wherewithal to move their daily diving operations to the South shore. Maybe some other day-dive ops too, but to ascertain a true day-to-day reliability of that product might be difficult. If possible, it is best to meet the boat on the South side via cab, you do not want to ride back home around the Western tip when there's a Norther. South side dive operations (from the three working AIs: BFK, CCV, RHR) are comparatively unaffected.
Does rain, in and of itself, affect diving? Well, sure it does. The best diving is always in calm, warm weather. Does rain affect the visibility? I suppose it does, but then you get into the never ending discussion about "the value" of visibility. On Roatan, it's 60 to 80' on a good day, but the treasure Roatan- it's unique offering- is the close-up macro stuff. You don't need much viz to enjoy that ! If your level of is affected by 150' + visibility, wait a while in your diving career before going to Roatan.
It's all survivable, so if that's your vacation time, go for it and hope for the best weather.