In Bioshock, you get plenty of choices to upgrade skills but it lets you have nearly all of them eventually. You don't have to worry much about putting a skill aside as you can easily reinstall it, and since there's no RPG-style inventory management screen, you don't need to decide what weapons to keep based on space; it lets you carry them all. Pure action fans might prefer these design decisions but those wanting highly consequential choices might find them a step back from similar Looking Glass Studios-inspired games.
To be fair, Ken Levine never did claim for it to be anything other than a first-person shooter, but since it's known to be the spiritual successor to System Shock 2, comparisons are inevitable. One aspect where Bioshock's gameplay is deeper is in the aforementioned hacking skill. When hacking a machine or lock, it switches to a puzzle/reflex mini-game similar to classics like Zenji and Pipe Dream, where you need to quickly move pipe pieces around to form a proper path for liquid to flow. If you fail to do this, it short circuits and injures you. I found the hacking to be a neat diversion but if puzzles aren't your thing, you also have the option of using money to unlock machines. So, in some ways the game offers more depth than its predecessors, in other ways if offers less.
Abundance of ammunition is another way Bioshock differs from similar games of the past. Ammo is everywhere in this game whether it's on enemies or for sale inside vending machines. This is necessary considering the game isn't really crafted for stealth gameplay. Besides not having to worry as much about conserving ammo, another thing that keeps the frustration factor low is that you resurrect at a Vita-Chamber when you die. In System Shock 2, there was a monetary penalty for doing this, and if you ran out of money, you could not resurrect again and had to reload a saved game. In Bioshock, there is no penalty other than being sent back to where the nearest chamber is. Between the large supply of ammo and the Vita-Chambers, the game is considerably easier than the System Shock games.
There has also been a lot of hype these past few years regarding Bioshock's A.I.. It doesn't revolutionize the genre but it's still an impressive evolution. Injured enemies use health stations, people on fire run to water, and the protectors of the Little Sisters (called Big Daddies) roam the halls to their destinations without collision problems, and will only attacked when provoked. Bioshock feels more real and alive than other first-person shooters.
Ultimately, that is why Bioshock stands out in an oversaturated genre. Rapture is believable as a dystopia both in the way non-player characters react within it, and how the environment and story elements let you see the effects of political corruption on a populace. It succeeds as an action game by providing an assortment of weapons and abilities beyond the typical gun selection of most first-person shooters. As far as inventory management, the effects of character upgrade choices, and difficulty level go, it does feel like some concessions have been made to make this game appeal more to the masses than in its spiritual predecessors. For these reasons, I don't think Bioshock manages to surpass the System Shock and Deus Ex games overall. Still, I did find it enthralling from beginning to end, and the fact that it deserves its place alongside some of the greatest games ever made is achievement enough.