This topic seems a little bit different from what I was expecting. I was hoping that this was referring to major franchises that need to be dethroned or dialed back to make room for new IPs, and thus to promote a more diverse future.
Instead, this seems to be more about games that one considers to be overrated (or incredibly popular compared to other titles in the series) that need to be outdone by another game in the same series. Hm...
Well, I guess I'll give my two cents about this. The games you listed won't be dethroned, they're classics, and in some cases they're legends. It's just like Adventure on the Atari 2600, it will always and forever be considered great, even if another title in the franchise were to come along and be better. Same with the Metal Gear Series. Metal Gear Solid was revolutionary for the stealth genre, as well as for video games in general (with it's voice acting which, at the time, was unparalleled). It's a classic, and even though the later games were great, and arguably better, Metal Gear Solid will always be considered such. Same case with Megaman 2.
Now let's take Pokemon. You know, I, too, would like XY to exceed the critical acclaim that GSC did, because I loved GSC and would love for another game in the series to meet it's calibre. I don't see that happening for two reasons, though. The first reason is because of what I stated above-partially. Not only is GSC a classic, but it's a timeless classic. I could easily play GSC from beginning to end without feeling generational whiplash. This goes for RBY, too. This segues into my second point, pokemon is slow to innovate. Very. That's the reason that RSE/DPP/BW/2 aren't as lauded as the first two, because they simply feel like pretty much the same game with a modern coating and a few new features in between, but not so many that you can play the first two entries and be blown away by "how far we've come". XY hasn't really proved to be an overhaul of the franchise, and it may be the same case as the others...but it could be better. Still, I don't think that it will reach the popular heights that GSC/RBY did, and that's a good thing. As long as those two stand on top, people will demand more, and the potential for change will increase.
With Final Fantasy, it's the old classic case, but with a twist. See, Final Fantasy VII is considered the most overrated title in the series, and I simply think that it's because it's most people's first Final Fantasy and because it was the first 3D Final Fantasy. The thing is, if you ask a Final Fantasy fan what their favorite FF title is, 9 times out of 10 they'll say Final Fantasy VI. Final Fantasy VII is so popular because of the time it came out, it's significance in Final Fantasy and Video Game History, and because it was a good Final Fantasy title general. That's why it's so popular, but I wouldn't say that it dethroned Final Fantasy VI or Final Fantasy IV. Those two titles are, to this day, the most loved FF titles, Final Fantasy VII is just a classic that happened to be the right thing to come out at the right time.
Ocarina of Time is the exact same case, almost to a T. The difference is, the chances that someone who played OoT had also played other titles in the series was much higher for Zelda than it was for Final Fantasy. OoT was still a lot of peoples' first, but if you'd asked everyone what their first Zelda game was, you'd get very mixed answers. Not to mention that despite OoT's popularity, Wind Waker, Twilight Princess, and especially A Link to the Past and Majora's Mask are contested for being the best in the franchise by the majority of fans, but it seems that in the case of OoT, people liked it more for how good it was rather than simply what it was, though both factored in greatly.
