It wasn't just the ending movie, the end boss was poor and felt out of place, and the last few levels were more linear and felt a bit lacklustre. Also the story twist was the same one from SS2.
There's a few other things too - the meaningless save/harvest choice - meaningless because it gave you adam gifts if you saved to make up for the adam you would have received if you'd harvested.
The other problem was the abundance of adam meant you didn't have to specialize. In SS2 if you chose to be a weapons guy, you could fully unlock maybe 2 of the 4 weapon categories, and your PSI, hacking, maintainance, repair, modification, research, stats etc all had to be neglected. So you couldn't see everything in one play through, the next time you played you could specialize in PSI, or you could max out your stats, or master the technical skills, or master the other weapons. Bioshock gave you enough adam to buy everything by the time you left a level, so it didn't feel like you were making any choices, and it hurt the replay value. Plus there were some other minor things like far too much ammo everywhere, repetitive hacking mini game, the silly camera research thing, plus the weapon mechanics felt a bit off.
Don't get me wrong, I did enjoy it, some of it a lot, but it wasn't quite the 96% game the reviews claimed. Like Oblivion it was compromised by needing to be simple enough for the console crowd.
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