Now that I am dreaming of the existence of my Bioshock 3, I've realized that we never see any animals in Rapture other than fish and dead kitties and the like.
Since this group that banded together and left Rapture for their own utopia without the fanaticism of Andrew Ryan chose a large island filled with its own population of wild life, we could have corals full of spliced up ostriches and wild boar. Much like with genetics today, they could have been using splicing to make their livestock grow faster, to have more tender and better tasting meat, etc. This is a theme that the original Bioshock stayed away from, focusing instead only on genetic manipulation in humans. Imagine being attacked by a stampede of spliced ostriches!
You could also wander into some laboratory filled with spliced bunnies and other monstrosities.
With a little creativity, it wouldn't be hard to find a new take on harvesting Adam. I'd like to thing this group started off more moral and the idea of using little girls as hosts was part of the reason for their departure, and so they've found a more clever and perhaps more complicated way of harvesting Adam from their slugs. Obviously this has a potential to hard to morality aspect of the game, but I still think they could come up with a fresh new take on the moral dilemma to replace the old "Harvest or Rescue" from the first two games. This game would have to be a drastically different take on everything from Bioshock. No rehashes, everything would need to be rethought up and re-conceptualized from the ground up.
Oh man, this game is so unbelievable amazing in my head! Can't wait for it to come out! (Too bad it never will) Suddenly Bioshock Infinite looks slightly lame...
Which leads me back to rehash a resent statement I made about how there is "nothing new under the sun" in regards to video games and nothing to get excited about anymore. Bioshock Infinite is the most interesting looking thing in all of E3 in my humble opinion, and it really looks just like Bioshock in the sky. I am sure I will play it an enjoy it, but with a release date being over a year away, I don't see much to get excited about it yet; it doesn't look like anything ground breaking or original which was a key trait to the original Bioshock.
Coming this year we have Gears of War 3, Modern Warfare 3, F.E.A.R. 3, Resistence 3 (wow, that is a lot of threes), Elder Scrolls V, and a bunch of other things that are rehashes of things that have already been done. Sure, they'll all have new features and no doubt old features will be vastly improved, but essentially they'll be nothing really that new.