My two cents as a long time stock WitP player (albeit a poor one), and AE co-developer.
AE is far from perfect (no game ever could be), but because of all the extra detail, the different map scale, the much-improved AI and so on, and so forth, I feel it's the superior game.
We're working hard on the first patch already, and if things go the way they're supposed to, you won't have to restart an ongoing game once you apply it. Jump in, the water is fine, and there's not THAT many sharks.
We are all dreams of the Giant Space Butterfly.