I agree that Banyan Bay is excellent for families or two couples, as the units are large (about 1,000 sq. ft.) and have two bedrooms and two baths, plus kitchen and living area. Really nice.
Xanadu is nice, too, though the units are smaller (the second bed is in a loft), but it's less expensive than Banyan Bay. The Palms is excellent, but it is right at the edge of town which may be a factor if you want to be away from town, and Caribbean Villas is well-run and in beautiful setting, though it doesn't have a pool.
Paradise Villas' two bedroom units to me are on the small side.
You might also look at Gaz Cooper's Playa Blanca on North Ambergris -- it has large condo suites.