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Well, a lot of the scale issues with MU and such are due to reusing parts - basically what Joes have done for years. That in itself isn't that bad, since we essentially get new figures that aren't simple paint swaps and it helps Hasbro keep costs down. (If Hasbro did all-new molds all the time, the toys would be ridiculously expensive.)

The problem with reusing parts in MU is that most characters in Marvel have unique characteristics that set them apart from the others in MU (Wolverine is short, Colossus is tall, Juggernaut is wide, etc.). And let's face it - the Marvel Universe is huge! But it's these features that make it hard to reuse parts.

With Joes, nearly all of the characters are human (or a close approximation) with millitary backgrounds, so it's easier to get away with parts reuse for the toys and accessories.