PokéBase - Pokémon Q&A
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Smogon's (showdown!) tiers are based off of use. People like heracross as a suspected mega instead of a regular mega I guess. The reason that regular heracross is OU and it's mega is BL is, like I said before, Smogon's tiers are based off of how much people use that Pokemon.

Basically, its because (1) some people use non-mega Heracross, making the total uses of Heracross greater than the total uses of Mega Heracross, and (2) mega-evolving Heracross uses up your mega evolution for the battle, and there are better megas out there.
To be honest it's really because regular Heracross is better. It has better abilities, better speed, and it frees up your mega slot for something more useful like Charizard/ Venusaur/ Scizor.