We did Belize earlier this summer and loved it. Stayed half at a jungle lodge near San Ignacio and half on Ambergris.
Rent a car. We used Crystal Auto because they set us up to cross into Guatemala to go to Tikal. The speed bumps are for sure serious business and are the reason that a 50 mile trip can take a couple of hours. But once you get a little distance out of Belize City, the pot-holed crap roads are much better. Many through the mountains look brand new.
Big Rock Falls was probably our favorite activity in all of Belize. Beautiful waterfall with deep cool water pools that we basically had to ourselves. For the last couple of hours in the afternoon, we did have them all to ourselves.
We also did Rio on Pools, another set of waterfalls.
Water taxi to Ambergris is about 1.5 hours. Not bad at all and pretty views. Definitely rent a golf cart if staying on Ambergris. The reef side is mostly unswimmable close to the shore (seaweed), but clean beautiful water is easily reachable by kayak or paddleboard. Snorkeling is fantastic. We did Mexico Rocks for a chance to see a manatee and for sure, one showed up.
Secret Beach is more like a Caribbean beach experience. Sand and clear water. Get there by golf cart no problem.