GSC were my favourite Pokemon games ever, right up to HGSS (maaaaaaaybe this is trumped by BW/B2W2 now, but still, I adore GSC).
As such, there is very little in the game that annoyed me. One small thing was the way Kanto was dummied down due to the hardware limitations at the time. It was unfortunate that the Seafoam Islands were just.. negligible, as well as Viridian Forest (not to mention the nonexistant Safari Zone). This was made up for with the fantastic remixes of Kanto's music, though, and so many other things.