There seems to be one main thing that annoys me from each generation of gaming.
2600/InTV
Shovelware. Horrible games that flooded the market and brought around the video game crash.
NES/SMS
Overly ambitious graphics. The games that knew the limitations of the hardware and worked within the limitations of the hardware visually stand up the best today, like Mega Man, Mario, Metal Storm, etc. Stuff that tried to do too much, like Metal Gear, often look muddy and awful by comparison.
SNES/GEN
"Every direction" sidescrollers. In the NES generation, most sidescrollers followed a linear path even when it scrolled up or down. In the 16 bit era, the map wasn't locked to one direction, and was instead one giant 'field'; we ended up with games that became a nightmare to traverse because everything looked the same and you had little clue to which direction was right. Stuff like Aero the Acrobat and similar platformers fell victim to this flaw.
PS1/SAT/N64
Bad 3D. This generation transitioned to 3D gaming, often because they felt they had to. Many 3D games do not hold up well at all simply because they tried to shoehorn 2D style platforming into 3D, usually with poor results. 2D games from this era easily hold up the best today, like Castlevania SOTN or even pseudo 3D games like Einhander or Tomba.
PS2/XB/GC
Stealth. It seems that many games seemed to force stealth missions into them. It works great in games that are centered around stealth, but felt awkward and out-of-place in action games.
PS3/360/Wii
Weak single-player campaigns. FPS games are most guilty of this, where the single player campaign suffers or almost seems like an afterthought in games that push online modes. Stuff like Bioshock from this gen seemed like a breath of fresh air because they made the game about the single-person experience, rather than tacking a single player mode onto an online-focused game.
What is your biggest pet peeve of each generation?