PC Gamer UK writer Tom Francis has spent more time thinking about those events than most of us, and he's posted his ideas for the kind of ending such an otherwise fine game truly deserved. The summary of his alternate ending is up over on his blog. There's some clever stuff in here; Francis manages to preserve the Big Daddy conversion, while turning mechanics like the Vita Chambers around and using them against you.
Tenenbaum manages to reach you on the radio for the first time since you entered Ryan’s office. Having heard about your command phrase, she asks if you would kindly DROP THE GODDAMN RADIO then meet her at her nearby hideout... Tenenbaum impresses on you that Fontaine is nearly unstoppable now that his genetic key is tied to Rapture, since Vita Chambers now work for him rather than you.
I like how this version of events makes the ocean more of an active threat than the sinister but more or less benign force it ended up being as the game was written. There's also what I would consider a more poignant and certainly more immediate moral choice than the mechanical Little Sister save/harvest option in the existing game, and some delicious irony in the last few moments.
Granted, hindsight is always 20/20, but this is a neat thought exercise if nothing else. Francis and some eager commenters have a good dialogue going at the bottom of the page dissecting his ideas and the way BioShock turned out, so if you have an interest in game writing and design--or if you're just looking for more BioShock to ponder until the sequel hits--I recommend you check it out.