I liked Yellow the most but my assumption is that it probably sold best (due to the Anime) and thus there are the most pre-owned copies of it.
OR, the shop owners are actually aware of the fact that to finish the game, you need Blue and Red, thus Yellow is the hardest one to complete since it doesn't fully compensate neither the missing Pokemon of Blue nor Red, thus practically when buying Yellow to actually finish it, you need three games rather than just two, but I doubt that's the case.
By the way, I personally loved the game, I bought it alongside a gameboy colour and whoever thinks it has anything to do with the Anime is currr-eh-zah. The only aspect borrowed from the Anime is Pikatchu who follows you around, and he's not even annoying, you don't have to talk with him. I think it's pretty cool. Plus, the game can be played *in colour* and that alone is a big selling point.
EDIT: Yeah, Manga books are comic books. A different artistic style compared to American comicbooks is irrelevant here.