For me i would say the most annoying thing was the glitches of course they weren't an issue until i discovered these with my brother online lol. Anyway as fun as they were they also killed the game experience. Up until i learned of them i played my games 100% legit and beat the game the only way it should be! After learning of these glitches though as a kid i would basically neglect all pokemon besides my starter and when i got far enough into the game to visit Cinnabar Island i would use rare candies and HP UP's on all the other 5.
It was fun but it really makes me feel dirty now thinking back to it lol. I have since returned to playing these games and doing it without any sort of glitch or cheat and the feeling of completing the game is so much more rewarding to me anyway.