I too have been to both Bonaire and Roatan several times and if I had to pick, I'd go to Bonaire. I like both places but I think the diving is a little better in Bonaire and I really like the shore diving. No schedule to follow. Get up when you want, eat when you want, DIVE when you want and as much as you want. No time limit on dives. No be back at the boat at a certain time. Hard to beat that.
Buddy's is hard to beat. I don't think there is a better place to stay than Buddy's. It's designed around diving and that's why people keep going back. The food is good there also. But check out Casablanca and Richards for some great dining in Bonaire and don't miss the beach cookout at Buddy's on Friday night. All you can eat fish, ribs, steak, etc.
If you do go to Roatan, I'd highly recommend staying on the Anthony's Key/Bay Island Beach Resort side. I have stayed at CCV and liked it but I think the overall diving is better on the AK/BIBR side. And I know the food is far superior at AK and BIBR as opposed to CCV. The food at BIBR is the best I have found of all three places.
That's my take on both places.
BDSC