Let's see. I'll try to limit myself to one per series.

Final Fantasy VII - yes, it's an important game that revolutionized not just the genre but the entire medium, but I feel it has too many flaws that many people just don't even remember. I consider it by no means a bad game, but its status as the sacred cow of the franchise is not entirely deserved, imo. Honorable mention: Final Fantasy X.

The Legend of Zelda: Ocarina of Time - once again, an incredibly influential game which probably wouldn't be even on this list, if it weren't for the fact that it laid the foundation for all the future games in the series, which I feel all do a better job at it in at least one respect, and yet they're not quite so revered. Honorable mention: The Wind Waker.

Breath of Fire III - by no means a bad game, but I never understood why it's considered the best one by so many. I feel IV does a lot of what it does better with just so many other elements added that fit in more neatly into my personal sensibilities, and it doesn't really have anything cool or interesting going for it like Dragon Quarter does.

The Sims 2 - this game was an important leap for the series, what with the shift to 3D and added aging, but much like other games on this list, I feel like its sequel just added so much more, so as to make this one nearly obsolete, yet somehow it's this one that's still considered the series gold standard for some reason.

Persona 4 - not the direction I wanted this series to take after 3, but I think what pains me the most is that (at least up until 5 got released) this was the most talked-about Persona, completely overshadowing 3, which is still my absolute favorite.