They weren't "made" by the same company; Irem designed the arcade game, while Nintendo did the NES port themselves. And much like 90% of the arcade ports in the NES library, I prefer the NES version better...
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My mantra, as worded by SamSpade on 06/12/12:
I don't resell to fund my collection, I don't treat this hobby like a second job, I don't care if my collection is worth ten bucks or ten thousand because I never plan on selling it. Seriously, what does the value have to do with anything if you never plan on selling? Speculation doesn't mean jack shit to me at this point, I just want to play my nes games...