Scott, the thing about SS2 is that, while the difficulty was certainly higher, there was no random respawning of enemies. This actually caused some heated debate. I liked it, a lot of others did not. Anyway, once you clear an area, it stays clear. You should be able to chip away at the difficulties until they're gone for good.
I've played Bioshock multiple times now. It has become some sort of obsession. There's a lot of richness in this universe, and I keep finding new things, as well as getting the whole picture more clear in my mind.
[spoiler]Ryan wanted to create a world where he could practice his ideals without intrusion. Objectivism pretty much defines those. It's roughly pure capitalism without any regulation or oversight from government, without encumbrances from any social agendas, and without any of what Ryan calls "petty morality"--no religious code of behavior to get in the way. He's fanatical about it, or became so in the process, and ends up rationalizing a lot of crazy actions in the name of preserving his ideals against increasing opposition. For objectivism to work, pure reason must be the driving force behind it. When humans, not gods, are at the helm, their emotional frailties eventually muck the whole thing up. (Communism has very similar problems.) Fontaine is a consummate crook, a very smart one at that. He plays a long con, years in the making, to take Ryan's world for himself. (I submit that, without a moral code, there is nothing wrong with this. It's just strong competition in a Darwinian system where all that matters is who is the strongest. There are hostile takeovers in the corporate world constantly.)
You, the player, are the result of genetic engineering, headed by Dr Suchong. You are only a few years old, but you grew and were indoctrinated at an accelerated rate. You were removed from Rapture, presumably to hide and protect you from Ryan. You were brought back as Ryan's assassin, and there was nothing you could do to prevent that. "Would you kindly go to Ryan's office and kill the son of a bitch." You could not resist this command, or even realize it was a command. After the fact, the German woman doctor figured out a way to undo the programming, and after that, you could act of your own volition. Your old master tries to destroy you when he knows he lost control, and you turn the tables on him. The end, with the little sisters as the only story element you really control.
As Que said, there are multiple ways to play the game. But once I figure out the best ways, it's hard for me to play it some way which I already know to be more painful. One thing I've gotten much better at is setting up the splicers to get mowed down by security machines. Last time I protected the lab in Arcadia, all I did was repeatedly project the target dummy into the middle of the room with the hacked security camera and turret. I just stood back and watched the action, only defending occasionally against the Houdinis. Sometimes they tried to heal at the hacked station, and scream out their last. Too entertaining.[/spoiler]