Although I did notice this back in the G/S/C days, I was never really that bothered, to be honest. I never caught and trained any pokemon at that point as I felt it was simply too late in the game.
As for HeartGold and SoulSilver, I'm of the same mindset, even though I haven't reached Kanto yet, and won't for a while, I already have six pokemon at most of them definitely aren't going anywhere.
.