Lacking knowledge in this area, it's hard to say; might have to do with the painting techniques he was using?
As contemporaries, although El Greco was only in his early twenties when Michelangelo died, I guess one would have less reverence for a fellow artist as one might have now many hundred years later.
Artistic exceptionalism. The painters I work with have nothing but endless criticisms and contempt for each other's thinking. "To them, all art stopped in $era. They have no appreciation or talent for $mystyle" is an incredibly common sentiment confided to one, given some time and not necessarily a willing ear.
El Greco saw himself as a master painter and colorist but Michaelangelo as just another passably capable producer of frescos and drawn bodies, a prolific grunt with no taste or style.
As contemporaries, although El Greco was only in his early twenties when Michelangelo died, I guess one would have less reverence for a fellow artist as one might have now many hundred years later.