Fallout Series - Some perks/skills feel essential regardless of the character type you wish to play as. They are also riddled with bugs and love crashing.
Bioshock - Combat feels incredibly clunky, aiming accurately is a nightmare.
Mass Effect series - Mass Effect 2's story was basically pointless, it didn't really continue from the first one as much as it did, fill the gap between the first and third. It's more like a "meanwhile". Mass Effect 3 had too many forced moments in regards to our characters. Moments that completely detracted from my Shepard and were entirely unnecessary for the plot, so had no reason to be forced upon us.
Gears of War series - Incredibly deep setting, but the dialogue and plots are extremely shallow and do not do the idea behind it justice. Those who have read the books will understand what I mean. The game had a lot of potential for a deep and impacting story, but they went down the wrong route.
Dragon Age series - The friendship system was too simplistic and easy to manipulate, the graphics were... not very good (although admittedly I didn't notice them after a few hours). The second had too many bugs, too many recycled areas and too many plot holes. It also held your hand too much.
Portal 1 and 2 are not on my list as they do not have any faults as far as I am concerned. They are not my favourite games, but I would not want to add or take anything away from them.
I can think of other games, but it said 5, and I am already cheating by using series for three of my examples.