Aren't they pretty much the same? The shows are the same. I think you can "dine with shamu" at either now. Both now have the Journey to Atlantis Ride. (This is one of the best amusement attractions I've been on, by the way, if you're into that thing. It starts off as a great flume ride, and then turns into a dry roller coaster; it's very well done.) Both have "shamu's happy harbor," which is a great play area for children. Both have the wild arctic ride/exhibit.
The animal attractions appear to be about the same -- you can feed dolphins at either; walk through a shark tunnel at either; penguin encounter appears to be basically the same at either.
I think the major differences are that at San Diego you can take the chairlift over mission bay for a small extra fee, and in Orlando there are additional thrill rides (e.g., a roller coaster).
I've never been to the Orlando one, though, so I really can't say from personal experience. Orlando might not have the tower that you can ride to the top of like the San Diego one has -- that's a really neat attraction, particularly if you go up during one of the shows and have a bird's-eye view.