Pac & JMM are evenly matched fighters Styles make fights. Beating or losing to one fighter doesn't make or break your legacy.
Then again, history has shown that high profile fights with controversial outcomes tend to go down in history as tainted. Occasionally. Mostly dependent on how big the fight was but that one definitely met the criteria.
Styles make fights and Pacquiao helped make Marquez into who he is. Outside of Pacquiao, Marquez has mediocre wins and losses against Chris John, Norwood, Mayweather, Pacquiao, etc. Anyone without any bias can see that Marquez was overrated as he was ranked #3 P4P prior to the Bradley fight which was ridiculous. I do think that Marquez's legacy took a large hit, but he is where he is supposed to be in the first place. I'm glad that he got exposed for what he really is before retirement, which is that he's a decent fighter but not any better than Erik Morales or Barrera.