First, the small bag size. Sometimes I felt like I was spending more time juggling items in my bag and PC than actually playing the game, especially when it comes to TMs. Like, I would get a nice and shiny TM and go to store it in my PC, but oh no! The PC is full! Oh boy...
Second are moves like Wrap and Clamp. While they don't do a lot of damage, especially on physically bulky 'mons, they unnecessarily prolong battles.
Third is the lack of a post-game or trainers stronger than the Elite Four. I'm the kind of person who likes to train their whole team up to level 100 after beating the bulk of the main game. I COULD do it on Gen 1, but wow would it take a lot of time and patience.
Fourth (and this is exclusive to Yellow), I hate how the Meowth, Ekans, and Koffing lines aren't in the game. I mean, I kinda understand why, those are all the Pokemon the Rocket Trio have and it would be kinda wierd to have the same Pokemon as them, but it's just so unnecessary, especially because I really like Meowth.
Fifth and lastly, the Exp. All. I am SO glad the Exp. Share works the way it does in future generations, because the Exp. All is just such an awful item, dividing exp. among all team members until the exp. adds up to basically nothing. I mean, it sounded cool at first, and I spent a lot of time catching a lot of Pokemon, only to learn that the Exp. All is essentially a throw away item and not even worth picking up and WASTING BAG SPACE.