I lived on Utila for two years and worked on the Utila Aggressor as well as at a dive shop, Utila Watersports and a resort, Laguna Beach Resort. Like others have said, it really comes down to if money is an issue.
On the Aggressor you do get more for your money. 5 dives a day (including night dives every night), meals, snacks, beer & wine and the crew spoils you rotten! You'll get to dive on Utila, Roatan, and Coco's Seamount (which land based don't do). The DM's tend to be better than a dive shops DM, but not necessarily a resorts. On Friday night (the last night) you get to have dinner in town and during the day you can walk around and experience the town.
I now sell for Laguna Beach Resort and if money is an issue, than this is still a great way to go. Here you get 3 boat dives a day, 2 night boat dives a week and unlimited shore diving. The DMs are the resort are great and good at finding creatures. You also get unlimited horseback riding, kayaking & biking in your package which is nice if you want a break from diving. Meals are included as well so only extras are drinks.
If you have any questions about either of them, let me know.