Khan beats John Doe Harrison in every shape or form. But I agree they should have just dropped the whole plot-twist angle. It wasn't a plot-twist. It was obvious over a year a head of time to anyone paying attention, and it added nothing to the movie.
If they would just gone Khan from the get go, I think everything would've been better for it. They could have honed Cumby's look a bit more, for one thing. But the big thing is it would have added badly needed publicity. The entire ad campaign (poster, trailers, commercials) would have all been changed for the better IMO.