1. FFXII = un-invertable camera... not a small quirk, dumbest decision ever
2. Okami = filter over the screen making it look "dirty", slow text, load times for EVERYTHING grrr
3. Lost Planet = why no 1-1 gun aim? what moron decided to do that?
4. Zelda WW = damn wind changing crap, the sailing would have been fine if it were just like more practical to change the wind direction
5. FFX = Tidus' voice
6. Zelda OOT = stupid chant in the fire temple, most offensive thing EVAR
7. Shadow of the Colossus = sometimes next to impossible to move around because of camera and controls, frame rate contributes to that
8. Mario Kart 64 = freaking moronic 5 second animation whenever you get hit, someone with three shells just moves up, waits, shoots again, you are f'ed
9. Gran Turismo 3 = the sense of speed (or lack thereof)
10. Medal of Honor = the clipping issue (you can never hit the damn soldier until after like 3-4 shots)
11. PD Zero = the horrible aiming/unstable analog controls
12. Devil May Cry = the lack of 3d movement mapped to the analogue stick ala Mario 64
13. KOTOR = the frame rate
14. Super Mario Sunshine = FLUDD, 'nough said
15. Gears of War = no 4-player split screen
16. Metroid Prime = scanning, 'nough said
17. Unreal Tournament = the physics... terrible... Quake FTW
18. Sim City 4 = endless micromanagement, no way to delegate those tasks to the computer and focus on the bigger picture and connect cities together and manage inter-city commerce
19. MGS2 = Raiden
20. DOA4 = button mashers can win
21. Ico = confusing level design at times, making you wonder WTF to do
22. Mortal Kombat = block button... WHY? Just WHY?
23. Madden = why no 4 player mode?
24. Anything by NST = art sucks
25. NES Zeldas = save system didn't necessarily work correctly, you end up losing all your stats
I think that about covers it fairly across all systems, developers and generations ;-)