I would add where when you kill the dragon you can fly it. How bad ass would that be?
I would remove the Sponge Block. That block has no point to it.
I would add a new nether boss.
I would add to where fish are visible.
I would add birds.
I'm not even going to argue about the ender dragon, I don't like it being there in the first place. But it would probably be pretty odd to being flying on an ender dragon, what if it flies over the void and like knocks you off or something?
Sponge block stays. Forever. It also does have a point, or at least used to (haven't tried using it in a while), because when you placed in in or near water, any water blocks within like a 3 block radius or something would turn to air.
NO NEW NETHER BOSS. NO BOSSES PLZ NO!
That would make fishing too easy.
That could be interesting if they were sort of just useless like bats, but they might get in the way a bit which would be annoying.