I’d argue it’s impossible for games like SOTN, Metroid Prime or Mario 64 to fit the topic when they are all evolutions of earlier series.
I really dig the more specific conversation of “which series peaked with the first entry?” because they highlight some interesting design challenges and the issues of how to approach sequels.
For instance, I would argue both Zettai Zetsumei Toshi and Metal Slug peaked with the first game, for almost opposite reasons.
The original Zettai Zetsumei Toshi was the most authentic interpretation of an idea, and its sequels tried less interesting new things while losing the element of surprise and novelty of the first entry (kinda the same issue which is blamed on Crash Bandicoot above).
On the other hand, Metal Slug peaked with the first game because the sequels did not really add anything notable to what made the first game so great but also didn’t really try anything different; they are just dilutions of the same idea over and over again (I guess they did add a more complex food mechanic down the road). Some episodes could be considered better than the first one depending on minor factors (game balance, themes, technical performance, which slugs you prefer) but they really are all more or less the same game.
What I find interesting above is that both series have the same designer.
Another good candidate for the dilution issue is Katamari Damacy. The original author was pretty much done with that concept on its first try. The other episodes are pretty good but almost feel like expansion packs or playable excuses for new soundtracks.
Crazy Taxi might be another good candidate. I prefer the mechanics and map of Crazy Taxi 2 but the first episode pretty much nailed it. I would argue however (uh, with myself? Well, I am French…) that the real but forgotten first episode in the series – the Street Fighter 1 of Crazy Taxi if you will – was Harley Davidson & L.A. Riders.