Chikorita is massively fucked over by how Johto is laid out and itself (stat and moveset-wise). It's unpopular not entirely because it's bad but because the region actively works against it. Bulbasaur at least has early game before it falls off in mid-game Kanto. Squirtle and Charmander eventually pick up after early game. Chikorita has none of that opportunity.
Like Charmander, the first two gyms actively work against your starter however; Unlike Charmander who eventually gets a leg up, Chikorita never has that opportunity. You're not really going to do much about Whitney, you can't do much to Morty and by this point you should have a solid team to deal with Chuck/Pryce/Claire which just causes Meganium to just kind of become deadweight. You do end up maybe having a good match-up with Jasmine, I guess?
Bayleef is one of the "starter" choices in Colosseum and it is kind of passable in but, you're trading a decent Fire-type (Typhlosion) or one of like, two (I think Quagsire gets surf but I could be wrong) Surf users in Colosseum (Feraligatr) for Meganium to attempt to "wall" or use status moves. When better limited options (like Forttress, who can explode) exists.
It sucks because I do like grass starters and I do like Chikorita. But it was destined to be only ever be used in the anime where none of this matters lol. No Mega/no alternate forms/no good HA/bad moveset/bad base stats. It's so over.