I'd have to say Final Fantasy VII and Zelda: OoT.. they stand out to me as the most overrated more than any others, I think. FF7 was great and I liked it a lot when it came out, but no more than the older ones really. Graphics and story have never stood out as overly important to me, so maybe that's why it didn't have as much of an impact. With Zelda I was so used to the 2-d thing and having it be quicker and more action oriented, and I just never caught onto the whole 3-d and focus on exploring large environments and stuff.. just didn't seem as fun to me.
Of course, none of that matters really.. everyone finds different things fun and won't agree on stuff like that. Truth is they weren't overrated, because a ton of people liked them. Just because I personally didn't doesnt devalue their popularity any.. so maybe overrated isn't the right word to use.
(First post here, by the way!)