The thing I hated the most about R/B/Y was the item system and not being able to hold more than 20 items was ridiculous I can't tell you how many times I would be in a cave or rocket base and have to leave to go empty my backpack in the nearest pokemon center. Even when I replayed Red last week, I couldn't store enough items in my PC.
Another thing I hated about Gen 1 was how necessary a guide was just do know what a particular move or item did. Sure you could trial and error, but how do I know for sure that I want to delete an old move for this new one when I don't know what this new one is. And this was before wikis or even gamefaqs.com and the only source of this knowledge was printed guides, but even then they were riddled with errors. I owned 3 different guides for R/B and a fourth for Yellow, just so I could be sure what was right.