When it comes to balance changes, I generally like the western versions better. Ninja Gaiden 3 and Castlevania 3 are a joke in their Japanese versions, in fact I'd argue that Grant is an improvement in the NES version.
But Bayou Billy/Mad City is indeed the exception, as far as I know it was one of the first games to receive such balance changes and they just hadn't figured out how to do it right yet.
Gyruss. I believe the Famicom version is missing the Konami code but the music alone makes it the better version.
And then there is The Bard's Tale. The US version was given half the rom size and is completely butchered. A real shame considering how starved for RPGs American NES players were back then.