Anthony's Resort with kids is definitely a good choice if you go during one of the weeks with a kids camp. They have a very organized and structured program from talking to one of the Marine Biologists at the Marine Sciences Institute (we sat beside her on the flight into Roatan).
The kids program includes dolphin training sessions, horseback riding, a visit to the Bird Park, and movie nights. You can probably do all of this on your own anyway if there is no kids camp. We also enjoyed signing up for the canopy ride after the barbecue at Tabyana Beach. One of the couples signed up for a whitewater rafting excursion and said it was not worth it.
The boat diving is awesome. The dive boats are very roomy and it is easy to get your gear and into the water. The conditions seemed to be consistently calm at all the regular dive sites when we were there in May. I don't think your 12 year old should have any problems. I would think the 9 year old would definitely be able to snorkel on the afternoon boat dives.
Our divemaster was Ricardo and we would recommend him highly. He was very attentive with the more timid divers and chose dive sites that everyone seemed to enjoy.
We were not as impressed with one of the instructors we witnessed giving a navigation course. She and her student surfaced a fair ways from the mooring line and our boat captain had to go and pick them up. The instructor admitted they had gotten lost!
The accomodations are basic bungalows and I would recommend the extra cost for the deluxe units with air conditioning. On our previous trip in December, we stayed in a standard bungalow and it was uncomfortable sleeping at night with only a ceiling fan. In May, we upgraded to a deluxe unit with air conditioning on the key and we took a 2 min boat taxi to and from the key by clanging on a tank... it definitely added to the charm of staying on the resort.
We enjoyed many nights on the dock watching the eagle rays come in to feed on the creatures attracted by the light. If you are looking for a laid back and quiet vacation then you will enjoy Anthony's Key. Don't expect a lot of other kids there if it's not during the children's programs. We are planning on taking our two girls (9 and 10) but the kids camps are always during their peak season rates!
Hope this information is helpful in planning your trip to Roatan. I'm sure you will have a great time!
the friendliest! 
don 
