I looked through all the Kanto Pokémon and found several Pokémon with noticeable differences.
(left is Ruby/Sapphire, right is Emerald)
Wartortle is more purple in Emerald (no, that's not its shiny form):

The outline around Caterpie's feet blackens (credit to Scorby). The far-side eye and tail-tip are also a bit different:

Lickitung loses the smile:

Jynx's skin tone is slightly lighter:

Snorlax speaks for itself:

I found no major differences between any Gen 2 sprites.
Even though you said you don't need all of them, I'm going to go through it anyway because why not. Gen 3 will be added when I have a chance to look through them.