We (me, MIL, DS3, DS1) went this week. I was surprised how busy it was, but then again, there were a lot of elementary schools there.
Here's how we tour:
Get to the park early, before 10 (usually opens at 9, 1st show is at 10). Grab map, head to Whale & Dolphin Theater to catch that show. While waiting, we plan out what shows we want to see & their times.
We then headed to the Seaport Theater to catch the dog & cat show (forgive me, I don't remember names of the shows).
After that, we headed to see Shamu's show.
The Sea Lion & Otter show was closed, as was the penguin exhibit, so we skipped those.
After those 3 shows, we headed to the exhibits we were interested in. We waited in like for the Turtle Trek just to see the manatees & turtles, but skipped the 3D movie d/t the ages of the kids. It would have been nice if they had made a line for those who want to skip the movie. It's kind of nuts to wait 20 minutes to see the manatees. When we were there in '09, hardly anyone was in the manatee area.
We ate lunch at Seafire Inn. It was decent. I remember it being better during our last trip.
We skipped the kids play area, we'll save it for next time. And didn't do any of the rides, due to the kids' ages, and the fact that I'm not into roller coasters much.