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More than "graphics", I think people are concerned with aesthetics. When you see the "soul vs. soulless" posts on this board, it is typically a comparison between what posters see as an overall drop in aesthetic virtue as the series has progressed into 3D.
I would tend to agree that graphics are not important, but aesthetic virtue is: a modern game can have intentionally minimalistic, low-bit graphics, but if it cultivates a cohesive, unique, and polished style enough to be immersive, then it will add a lot to the experience.
PKMN has largely lost its aesthetic, and indeed, this seems to have occurred in the transition to 3D. The art style in the newer games seems derivative and uninspired, and the lacking graphical quality, as well as the visual glitches, is just a knife-twist for a lot of people. Game Freak could have taken a more stylistic approach with the jump to 3D, and really solidified a new identity for the brand, but instead they went with a hacky, generic, and safe art direction without the competency to really bolster it with strong graphics, so it falls flat, and takes players out of the experience.
