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Why did Gamefreak hate it so much? It's cute but it sucks terribly. The best thing I can say about the Chikorita line is that Meganium was usable in Gen2 OU but after that... yuck. In the original GSC it was clear that they hated him with all the gym leaders with type advantage and all the poison types in the Rockets' teams, but HGSS was when they decided to publicly bully Chikorita since they negated it the egg move Ancient Power as a level-up move to make the first gym easier (remember when they gave Charmander Metal Claw?) and they barely updated its movepool (still bad coverage and the most notorious additions were Aromatherapy, which doesn't matter in-game, and Petal Dance, which locks you into a STAB that is resisted by 7 types and with 90 BP it isn't scaring anyone coming off 83 SpA). But the worst part has to be Red, who has auto-hail in his battle and half of his pokemon know BLIZZARD, one of them having STAB and of course we all know (or should) that Meganium's struggling to OHKO Lapras.
The moment they decided to make Reflect and Light Screen into TMs was the moment they decided to make the Chikorita line hopelessly outclassed and it just keeps getting more pitiful with all the powercreep. If there's a mon that should have gotten a mega it's this one, and not only because Mega-Meganium has an awesome ring to it. Worst part is that starters are supposed to be reliable in-game.
