I don't really want to answer with no more inforamtion then 'Because Game Freak wanted it that way' but I might be forced too.
If there is any logic, it's this. Defeating Brock in Red/Blue with Charmander and the other early-start Pokemon alone was near impossible, you'd have to over-level a good 5-9 levels and get lucky with your Embers. They wanted to make this not as prevalent in FireRed/LeafGreen by having Charmander learn Metal Claw. After this, however, there's really no reason to have it learn Metal Claw, because any other Gym it struggles with can be countered there from in. And it doesn't appear as an early on Pokemon in any other game, if it does, it doesn't need any assistance. Though there's still not much reasoning to why they took it out instead of just leavign it in.