The sea cabs cost money to maintain and they ultimately only saved you about 10 steps of walking so there was really no point in keeping them open. It was the shortest ride in WDW (that actually goes anywhere), I believe.
The manatees are back as of last week. They continually rehabilitate and release these so that's why they may not have them every time. The tank also featured at least two dolphins along with the sharks, rays, etc.
The pavillion was filled with people when I was there last week. The kids (they were everywhere) really loved it. Much like AK, most adults have seen so much in real life and on TV that seeing those fish really doesn't do anything for them anymore.
Some folks will tell you that LS is empty after 11am. Well guess what? So is the rest of future world aside from Test Track.
I would be more than glad to have a cool new attraction in LS but I maintain my stance that there's nothing "wrong" with it the way it is now.