Well, the story and such was fine, it was all mechanics for me. A lot of this I posted back in the "What will you never play again" thread like 6 months ago, but I'll sum up some of it here.
The minigames for bypassing, lockpicking, and hacking? Well, lets just say one made me pull my hair out in frustration.
The skills available to customize what your character is good at? Anything not a gun related skill is essentially useless. Stealth is iffy until its highly invested in, because cover does jack squat (you'll find this out in a firefight too), and even then is only good up until you get to a boss fight. Melee is only useful against single, isolated enemies.
As you progress through the game, the load times get absolutely horrendous. And I'm not just talking about during levels, I'm talking about loading up the shop, which is just text and some graphics. And that is even after I tweaked the config file to improve things.
Most of the time I can sit through flaws and bugs in a game's engine if I am interested in how the story turned out. I think this was the first time I went "Screw it, I don't care how it ends, this is just too much."