Most of them, honestly.
When you look back, it was cool what they were doing at the time, but progress is such that all newer games have iterated on those groundbreaking formulas and improved upon them, making the older games seem less spectacular than they were at launch. I have fond memories of playing PS2, N64 and Dreamcast, but when I go back to play some of those games I enjoyed as a kid, I find that there's always something super sub-optimal like the controls or some arcane mechanic that doesn't make much sense. I find this to be the consistent issue going back to PS2 era and earlier.
I think the PS3/360 era is the one I have the most nostalgia for all things considered. There were a lot of stellar RPGs like KOTOR and Mass Effect that generation. Stuff like Red Dead Redemption was coming out. Control schemes finally became generally standardized and understandable. Tutorials, saves and decent graphics were really finally all combined properly for the first time.
I find the same sort of issue with movies. When you go back passed the 80s, you start hitting pacing issues. Same with video games. When you go back passed the mid-2000s, you're going to run into early installment weirdness.