>>48242136Charmander gets access to a good variety of moves between its level up learnset as well as TMs. Particularly having Mega Punch and Dig early on is pretty strong especially since Dig has 100 base power in gen 1. You can even have some interesting sets with things like Swords Dance. Not having a STAB move better than Ember for a long time is admittedly a flaw but you really don't need one with how good the other options available to you are. You could even replace Ember with Dragon Rage if you want which could hold you over until you get the Fire Blast TM.
Chikorita on the other hand is a Grass type with almost none of the perks of that typing. It had the unfortunate act of following up on Bulbasaur who had great options like Leech Seed and Sleep Powder. The only powder move Chikorita has is the lackluster Poison Powder and while it does have Leech Seed the only way to get it is through breeding. Grass/Poison is in my opinion a preferable typing to pure Grass for in-game purposes. Without it you have to deal with things like Chikorita being vulnerable to poison. Grass is also just a worse attacking type than Fire. It kind of worked out in Red/Blue when the first two gyms were weak to Grass, but Johto is extremely harsh on the type in a much worse way than Kanto was on the Fire type. In terms of moves and utility Chikorita is more or less limited to setting up screens and not much else.
tl;dr Kanto gives Charmander more flexibility that makes up for the unfavorable matchups it has early on. Johto on the other hand gives Chikorita far less to work with to the point where it becomes less of a hard more and more of an artificial handicap.