I'd suggest Blue Angel. The hotel is on the water, and every room has a balcony to enjoy the view. It's not luxurious, but very clean and a great place to stay. The on site restaurant serves breakfast (usually included in their room packages I believe), the lobby has coffee made however early you ask for it, and there's fridges in the rooms. The dive op has multiple boats, so they can split groups by experience. They do have a few large boats, but I've seen those used primarily for groups diving together, and their mid day mixed dive/snorkel trip.
The typical profile for a 2 tank dive in Coz is a deeper first dive (70-90 feet) to a wall or large reef where the topography is the main feature, and a shallower second dive (40-60 feet) where the marine life is more of a feature. Obviously that isn't true of every dive trip, or every op, but it's what seems to happen most often.