AS said, the faulty with this, which I always say is identical to Stalkers problem, was both companies wanted to make an RPG, failed horrifically, kept in the player being able to MASSIVELY increase his stats, strength, defence, health, power etc, while none of the bad guys get such large increases. In both games 20% into the game you are next to immortal and you lose the need to be creative or put in effort to kill anything. The lack of seriously harder gameplay anywhere throughout either game, with similar/same bad guys from start to finish left sorely threadbare gameplay.
The fun in most games is powering up stats, or getting better weapons, only to face better opponents and more puzzels to thwart you. Both games completely forgot to scale the difficulty of the game, something thats been fairly standard since the beginning of gaming. Frankly IN Bioshock from around half way through you can kill everything, easily with just the wrench which is just a touch pathetic. There might be loads of plasmids but almost all of them went unused. Wait a minute or two for a big daddy to walk near someone you could get to kill him, or walk into a puddle to fry him, when you can just run up and smack him one.
Every new plasmid I'd use it for 2-3 kills, get bored, switch to the most standard fast acting ones and power on through.
Story was poor and I can't remember a game with such a truly ridiculously easy end game boss. Remember the days of multiple tries learning the sweet spots to hit boss's and how to kill them. With bioshock i remember, standing back, shooting and it being over and thinking, WTF... with a pretty awful end story aswell. While the graphics weren't in any way fantastic, its what you do with it that counts. GTA4, billions of light effects and a awful looking game. Bioshock, really quite weak texturing but a brilliant overall effect from just great design. Shame the story/gameplay ruined it.
Most people just felt it was a chore to finish the game, where as with say COD4 i was pushing through the game wanting to see what happened next and was dissappointed when the game finished, in that I couldn't keep going, as opposed to being relieved I was finished and could go play something else.
EDIT:- I guess something that was wildy needed in both games, and games like Crysis, was far more varied enemies. You want the esculation of difficulty, harder guys with more attacks, more weapons to use on you. For Bioshock you i would think needed another 4-5 enemy types at minimum throughout the area's, and you'd want one to be highly susceptable to frost, one who would triple in strength when in Rage and attack other guys, one who hates fire goes mental and sets others on fire. You need things like plasmids to be the only way to kill certain people, rather than a slower alternative to a basic easier quicker attack. There was just no variation. Again looking at COD4, you weren't always doing exactly the same thing, sniper level, the plane bombing level, varied terraine and varied fighting styles, city, field, fighting on the run or from a defendable position. Bioshock was, after 1-2 hours in, run in smack everything done.