Hmm.. lets see...
Training a Ledyba that only knows Tackle, then learns the useless Supersonic, then Comet Punch, none which are any use on it, since it can't attack, and even when it evolves, it's still hopeless...
Sneasel's backwards stats
Poliwrath not getting any decent fighting moves in GSC.
Haxy Computer crit hits, always hitting Supersonic that is effectively Confuse Ray #2, etc...
Finding legendary dogs when I have no Pokeballs
Pokemon who appear when you don't need to or want to find them
Training Magikarp
Gyarados' Special Attack being piledrived through the floor in GSC and beyond
Machamp having less attack than Dragonite
Machamp not having +300 Special Defence, it should have higher
The RBY hax Poliwag/whirls that use 100% accurate Hypnosis and when you wake your Pokemon up, they use it again, rinse, repeat
Seeing really cool Pokemon such as Dewgong or Kingdra being shafted continually, same with Hypno, whereas Alakazam and co get all the fitting moves, and Hypno's stuck with Insomnia, and so can't us Rest easily, it's only recovery move!
Yellow Pikachu: it's yellow version, but Pika still sucks
The insane slowness of most of the Pokemon I train, and so can't run from Golbats
Having to dump Feraligatr/Slowking/ water Pokemon that can't learn Waterfall in GSC and get a Poliwag just to get through Tohjo Falls, and then have to try and avoid as many trainers as possible as I only have 5 decent Pokemon.