Rotan is a lot easier to get to as there are direct flights from Houston. To get to Utila one lands at San Pedro Sula on the mainland and then takes a somewhat expensive (for the distance) flight the rest of the way, unless you have a lot of time to go to La Cieba and take the ferry.
Personally, I prefer staying in West End on Rotan to all of the possibilities that either Utila or Roatan have to offer. Utilla, in the town, has a dive school mentality. You could actually be told you need to have an instructor with you on a night dive if you never bothered to take a PADI advanced, even if you have 100+ logged dives. The town itself is a bit primitive.
Some other ideas:
Laguna Beach: I have been there twice. It was great when Liz (now manager of CoCo View on Roatan) ran it, and the second time it sucked with younger managers. Its isolated.
Utila Town: Despite the dive school mentality, I enjoyed 2 weeks of diving with UDC and staying at Ruby's. Its cheap, but a bit primitive. Its a very young backpacker scene in town.
CoCo View: Expensive, but a great place to go if you want to pack a lot of dives in and only have one week. Its possible to do a shore dive whenever you want. Its a bit isolated, and pretty much lights off by 9PM. I was there once when Mr. Bill ran it. We could not leave the island due to bad weather and he gave everyone 2 free nights with meals.
Fantasy Island: Priced attractively, I have been there 3 times. The last time I thought the crowd was a bit rough. Not as Isolated as some of the other all inclusive dive resorts.
West End: Reasonably priced hotels, cheap diving ($25 per tank if you do 10 or more dives). Decent social life, lively bars and several good restaurants. Not as cheap as Utila town, but much less expensive than just about anywhere else in the Caribbean. Its my new home away from home, with 4 trips in the last 18 months.
Anthony's Key: Expensive but very nice, fairly close to West End. Still the lights tend to go off early as in most of the other all inclusive dive resorts. I have not been there in about 8 or 9 years.
West Bay: Avoid, its overbuilt and expensive, although there were some great deals offered to Canadians a while back.
During ther summer especially the bugs bite like crazy, and I really think they are worse on Roatan.