I more often see the reverse. If I say Ocarina of Time is my favorite game (and it is), and that I think it's the most well-made Zelda game for its balance of gameplay elements (and I do) there's a knee-jerk reaction on the part of many gamers to claim that I simply prefer it due to nostalgia.
The funny thing is that if I claim Mr. Smith Goes to Washington is my favorite movie (and it's close), movie buffs wouldn't give me the same answer.
If someone states that they prefer a game due to nostalgia, that's perfectly fine because that's their personal response to something. If they state that they think a game is better than others because they're nostalgic about it, that's inane, and their statement should be criticized as such.
But don't infer that people who like an older game enjoy it simply because of nostalgia. I never owned an SNES, so I didn't play some of my favorite older games until the end of the last decade. Nostalgia plays no role in, for example, Final Fantasy VI being my favorite FF game. But if I were to say I enjoy it much, much more than FFX, both of which were released before I touched a single FF game, I'd face accusations of nostalgia.
I'll add this, and it's a matter of personal preference: I love RPGs, adventure games, and platformers. I don't care for FPSs. If I had been born ten years later than I was, I likely would have had far less of an interest in gaming because, all other things being equal, FPS games would never have engaged me. Arguably my first major game was Wolfenstein 3D. I played it before I played Super Mario Bros. While I enjoyed navigating the maze-like first and second level, I never had fun with the actual shooting. Even post-Doom, there were very, very few FPS games I cared for, and I've tried many. So when I say I prefer earlier eras, particularly the pre-Xbox 360 era, it's not strictly nostalgia. It's also the fact that games I like aren't as widely represented anymore. After Sega went belly-up, the industry moved in a direction that does not appeal to me.