Wario is arguably better known for the Wario Land and Warioware series where he's not a villain. A starring role in two different series trumps one game (Mario Land 2) and assorted non-canon spin-offs IMO.
Waluigi only has the spin-offs and I don't know enough about his actions there to judge, but I see no problem with only removing Wario.
Actually Wario might have been a villain in Wario's Woods and some JPN Exclusive game where he kept dropping buckets on Mario's head. Might not be as clear-cut as I thought.
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In this world which will someday fall to ruin...
...dreams and hopes don't matter at all.