I'll add my two shillings worth:
I've stayed at both, Chaa Creek a number of times and Ek'Tun once.
They're both really great places, but different.
Both are on the Macal River but Ek'Tun is more isolated. You can't drive all the way there -- you have to park and go across the Macal river on a little boat.
Ek'Tun only has two cabanas, whereas Chaa Creek has a couple of dozen units, mostly in duplex cabanas but there also are deluxe garden suites.
Ek'Tun was until recently run almost entirely by Phyllis and her husband (they've split up) with part-time local help, whereas last time I was there Mick Fleming told me they employed about 70 staff altogether at Chaa Creek, including grounds and spa workers.
So it's two very different experiences. Ek'Tun is more like a B&B. Chaa Creek is more like a small resort. Some people like the B&B atmosphere, where you eat with the owners and do about everything with them, and with the maybe two other guests who are there at the time, but others may find it a bit claustraphobic, especially after a few days. At Chaa Creek, there are always a number of other guests, whom you may get to know over drinks or dinner, and you're not locked into a tiny group of people with whom you may or may not share anything.
There's also a lot more to do at and around Chaa Creek -- there's a beautiful spa, the medicine trail (though it's temporarily closed), horseback riding (Ek'Tun may offer that again but when I was there they weren't), a Maya farm, a butterfly centre and natural history centre and lots of planned hikes and tours.
However, there's a lot you can do a Ek'Tun, especially for active, fit people -- hiking to remote caves, for example. And Phyllis can arrange just about any kind of tour.
Ek'Tun does have something that Chaa Creek doesn't -- a fantastic natural swimming pool. Really one of the best pools in the country. You can probably even skinny dip there, just you and the howler monkeys.
The grounds of both are beautiful. Ek'Tun's are more natural, but lusher and more like a jungle. Chaa Creek's are carefully manicured.
Food at both places has been good when I was there.
I really like them both and would go back to either in a New York minute. I guess I would say that Ek'Tun is in some ways more special, unique and small, but not everybody would like it.
Belize books and publications by Lan Sluder:
Belize First Magazine (http://www.belizefirst.com
Fodor's Belize & Guatemala Guide (new 4th edition coming this summer)
Adapter Kit: Belize (the first and only comprehensive guide to living, retiring, working and investing in Belize -- a best-seller on Amazon.com)
San Pedro Cool (the first and only visitor guide to Ambergris Caye)
Belize First Guide to Mainland Belize
UpClose Central America
Belize Book of Lists