When I was younger, I guess Miltank was my only problem, since I was a beginner. Last time I played Silver, she turned out to be really easy. Never knew how useful Rage could be. And to be honest, I found out recently what Rage exactly does. Before that - I rarely used it.
Now the things that annoyed me few days ago when I played Silver again. The thing that annoyed me the most are those places that need a dozen HMs, like the cave with Lugia and the path to Kanto. I mean, at the end of the Victory Road, Silver awaits you. You can be really handicapped without a Pokemon, unless your team's great. But still, better have the sixth ranger than not.
Also, it kinda annoyed me that Silver's awesome theme is lagging. The music starts playing few seconds after his appearance, when he gets close to you and starts talking. Blue's theme at least played when he entered the screen. It really annoyed since the song is good, and I mostly skip the dialogues when I replay or rush through games.
And also, Mt. Silver. Last dungeon. What do you need inside of it? FLASH. Thankfully, I can look up the map on the net, so I can easily walk in the dark, but without it, it'd be really annoying having to take only 5 members once again. And erasing one of your great moves for Flash just kills the game.
Although Kanto was a bit lack luster nowadays, it was still a great feat back then, and we can easily ignore the lack of challenge and boring stuff in-between. It's post game after all. If they created a story for Kanto too, it wouldn't be a post-game anymore, but the real game. Still, the gyms were too easy. They should have raised the levels, at least by 2 for every next gym. The only challenge was Blue, since he had a mixed team. Others were too easy. And of course Red, the weakest of them all (j/k). My Pokemon were mostly in their fifties, and still kicked his ass. I only lacked moves against Snorlak and Blastoise, so they were a problem. Mostly since I played Nuzlocke. If I played like normally, they'd be easy too.
Aside from all these things that annoyed me, it's still one of my favorite Gens. Or maybe I just love them all :3