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The art direction was inconsistent. The first episode made towns and cities bigger than they are in the games and changed some stuff around to make the pokemon world look more lively, but from the second episode onwards they made the pokemon world look exactly like in the games.
Red didn't seem to improve as a trainer, he always relied on the power of friendship and his charizard's strength.
It felt as if the writers couldn't decide on whether it should be a gen 1 anime or not. Sometimes it felt like it was gen 1 (Oak says there's only 149 pokemon, jolteon doesn't have its ability and red used a bunch of fast pokemon in the league), but then we see charizard mega evolving, haunter using shadow punch and, well, everything looks like in FireRed/LeafGreen rather than Red/Green
