Gold and Silver have a lot of these, which unfortunately encompasses the majority of new Pokémon, but I wanted to focus specifically on a couple of these that are rare more from location rather than encounter rarity.
Natu and Smeargle are only found in grass outside the Ruins of Alph, grass that can only be accessed by trekking through Union Cave. Said cave is one of Johto's two required caves, but what you're required to navigate through is a pretty straight shot. You can also bypass it most of the time after you clear Sudowoodo out. If you didn't do what little exploring you could in Union Cave the first time or missed the dialog from a trainer mentioning roars from a Pokémon deep in the cave on Friday, you probably wouldn't think to return once you have Surf (which is received after you clear Sudowoodo). If you didn't explore or forgot the little hints, there's not much incentive to ever return.
Let's say you're a trainer who wasn't planning on going back to Union Cave. You keep playing your game until you hit Route 44, and you fight Birdkeeper Phil and his funny round bird Pokémon Natu. You check the Pokédex to see where it's found, and it's... the Ruins of Alph? The only thing in the caves is Unown, and no grass is immediately visible. There's an apparently inaccessible cave visible to the left of the east entrance; its connecting cave is either barely or barely not visible by surfing along the water on the north part of the map (still no grass). You will have no luck trying to break down the caves the Unown reside in to get to what you can tantalizingly see.
Union Cave is very close to the Ruins of Alph, and it's possible you could see how the two might be connected (it has "union" in its name, implying some sort of connection to something else). But it doesn't change the fact that Natu and Smeargle are hidden in 12 patches of grass total in an area you have to get to via a cave that isn't where the Pokédex lists them at.
Natu and Smeargle are only found in grass outside the Ruins of Alph, grass that can only be accessed by trekking through Union Cave. Said cave is one of Johto's two required caves, but what you're required to navigate through is a pretty straight shot. You can also bypass it most of the time after you clear Sudowoodo out. If you didn't do what little exploring you could in Union Cave the first time or missed the dialog from a trainer mentioning roars from a Pokémon deep in the cave on Friday, you probably wouldn't think to return once you have Surf (which is received after you clear Sudowoodo). If you didn't explore or forgot the little hints, there's not much incentive to ever return.
Let's say you're a trainer who wasn't planning on going back to Union Cave. You keep playing your game until you hit Route 44, and you fight Birdkeeper Phil and his funny round bird Pokémon Natu. You check the Pokédex to see where it's found, and it's... the Ruins of Alph? The only thing in the caves is Unown, and no grass is immediately visible. There's an apparently inaccessible cave visible to the left of the east entrance; its connecting cave is either barely or barely not visible by surfing along the water on the north part of the map (still no grass). You will have no luck trying to break down the caves the Unown reside in to get to what you can tantalizingly see.
Union Cave is very close to the Ruins of Alph, and it's possible you could see how the two might be connected (it has "union" in its name, implying some sort of connection to something else). But it doesn't change the fact that Natu and Smeargle are hidden in 12 patches of grass total in an area you have to get to via a cave that isn't where the Pokédex lists them at.