People like to point out NES games that took wild liberties with their arcade source material. Like… Bionic Commando! (Actually, a sequel to the arcade game.) And… Strider! (Actually, a completely different game altogether.) OK, so maybe that whole phenomenon tends to be overplayed. But Rygar — now, that’s a valid example. It was basically a dull Rastan Saga clone with a beautiful sunset backdrop in the arcade; on NES it was remarkably metroidvania-esque, with the addition of a top-down element linking the various world areas together. A little flaky in the programming department, but otherwise a fine creation that was way better than its source material.
The other noteworthy radical NES reworking was Ninja Gaiden, of course. Which was also from Tecmo. There must have been something in the water over there.