Yeah, Hush doesn't count. The original story presented HUSH as a new villain and the finale presented him as being Tommy Elliot, this new supporting character inserted into the backstory.
Xorn and Magneto is a good example from recent Marvel history. Morrison introduced Xorn, this new Chinese mutant with a cool mask and presented him as a good guy. What helped was that Morrison introduced many new characters in his run, and so Xorn seemed to fit in with the new class of characters. The way Morrison of course executed that denouement though ruined his entire scheme.
There are other examples I am sure.
-- The Thunderbolts Issue #1 is a good example of this being done with a whole team. An entire new team of superheroes was promoted in a build up to issue#1 and then it was revealed that this is the Masters of Evil in disguise.
-- Technically Red Hood being Jason Todd? I mean the original "Under the Red Hood" story had Red Hood introduced as a legacy villain, someone taking over Joker's original identity. And then it was revealed that it was Jason Todd resurrected.