I spent a month with Deep Blue Divers, the in town shop, not the resort last Jan/Feb and I was more than impressed. Mind you, I was only interested in doing a couple of dives a day. Surfing their website, I see that their staff has turned over but if the same woman who is running the place, is still running the place, then I'm there again next Jan/Feb without even looking at the competition.
However
Were I to find myself in a situation where I needed to look elsewhere, then my first choice would be Alton's. Rob, who posts here, says all the right words, one hour dive times, dive boats with divers sharing a common level of experience ( it sucks having to end a dive with 1200 PSI in your tank because some guy in the group sucked his tank dry ) and...free t-shirts.
Alton's has a very appealing deal offered in the trips and marketplace section.
So if you're willing to pay for the Lighthouse Hotel would you consider doing an all inclusive ? Deep Blue resort has (had ?) a special which when you add up the cost of dives, hotel and food, meets or beats staying "in town"
Want to stay in town ? I've never heard anyone say anything bad about UDC ( except me

and that was a "personal" issue which had nothing to do with their quality of service ) and the Mango Inn.
By and large, all of Utila is about selling courses with very little focus put into marketing the place as the inexpensive and appealing dive holiday destination that it is. Conventional wisdom would have you showing up in the island and spending half a day interviewing dive shops to see which one(s) meet your needs and wants.