I'm sure part of it is "Nostalgia" because I grew up with the NES, and the SNES in my teens, but in general, I've always preferred sprite based and 2D gaming, not just because I liked it as a kid, but because I still prefer it now. Sprites, especially for side scrollers, 2D fighters, old school Zelda style games, etc., always seem to work far better than polygons, far tighter, more precise controls/gameplay, etc. Plus it's just more aesthetically pleasing.
It also bears saying, though many have said this, that old sprite games, hell even old 80s games, often still hold up today. Whereas polygons age badly, espcecially that first Saturn/PSX/N64 gen. What we thought looked "good" back then, looks like blocky ass now, and even the following gen still often looks pretty rough, depending on the game/developer. But with older sprite games? Many old PC/Arcade/NES/SNES/TG16/Geneis/Etc. games still look really good, to this day.
Beyond all that though, yeah, I would say that out of my Top 10, or even probably Top 30 or more favorite games of all time, I'd be willing to wager that most of them are probably from that era, classic arcade, PC, NES, SNES, etc., or something like GBA, or modern indie games like Cave Story or Shovel Knight. What can I say? It's just my style. Don't get me wrong, I love a lot of modern 3D games (and even PSX/N64 era ones), but I'll always prefer 2D over 3D.