Gnarlysb:
I was on the Pilot in Belize over Xmas, and the Sun Dancer II about three years ago. Both are great. The decor in the cabins and public areas is definitely more upscale on PH, but I found them both to be about equally comfortable in terms of accommodations. The crew on both boats were professional and great to spend the week diving with. The big thing I love about the Nekton boats is they are MUCH more stable (not to the point where you can't even tell you're on the ocean, but way better than a single-hull boat). To me the biggest advantage to this is when everyone's getting geared up and ready to get into the water -- much easier to cross the dive deck with a tank on your back if the boat's not rockin' & rollin'.
New diver on your own on a liveaboard.... If you're not bringing your own buddy, you'll be looking to find others on the boat to dive with. Sometimes this is easy, sometimes insta-buddies don't work out so well. Both boats will provide DMs to dive with at least some of the time (I don't know if they can spare DMs to dive with someone five times a day, though). As a new diver, I'd recommend trying to get to know the other guests as much as you can early in the trip to figure out who's going to be compatible to dive with. I try to look for people who have experience, know what they're doing, and have a real love of diving. I think you'll be fine.
I've never been diving from Ambergris Caye, so I can't speak to the dive sites. To me the main advantages of liveaboard diving over resort diving are: more dives per day, access to more remote sites, and no schlepping gear all week long. Just roll out of bed, grab breakfast, and go diving!
FWIW