I can think of a few.
A chunk weren't available til you beat Johto and burn through Kanto like
>>27035985 said, including stuff like Murkrow and Misdreavus or appeared lategame by the 8th gym like Phanpy, Teddiursa, Skarmory, Gligar, Swinub, Delibird.
Most evolutions to previous gen mons required you to trade with an item you got pretty much after the E4.
Babymons were made but not available in the wild, you could find a Magmar in burned tower but not a Magby. It may as well have not existed.
I think what is sort of worse though is that a good chunk of mons didn't exactly have good stats to use either compared to how it was in gen 1, especially most that didn't evolve. e.g. Qwilfish, Murkrow, Sudowoodo, Aipom, Corsola, Aipom, Yanma, Delibird, Dunsparce, Smeargle, etc.
You couldn't really take those so far without it seeming off. At least in gen 1 you had mons like Tauros, Magmar, Electabuzz, Pinsir, Snorlax, Aerodactyl, the hitmons and so on which were pretty useful all round.
Not to mention there were a few gimmickmons like Wobbufett, Shuckle, Smeargle, Unown and Delibird.
TL;DR: We got new mons, but only a handful were there for us early on like Hoppip, Wooper, Mareep, Heracross and early route bugs, they're seen as more popular between people because they were available pretty early to players without bullshit.
