Everyone has a POV. Some may be alien and incomprehensible, but opinions they be. Oh well.
I have been a Scorsese fan since I was in my teens, but I can see why some people would not like those films(apart from the Aviator, I have not seen that yet, i have a bootleg disc of it that does not play right, i think it has germs on it).
There was a guy on another forum whose opinion I respected a lot when it came to films, and I recall him saying he didn't like certain Scorsese films, I was surprised and asked him about that and it turned out he didn't like any crime/gangster film made after the Hayes code came into play. The fact that he felt some filmakers glorified these types of people rubbed him up the wrong way, so he could not enjoy the films.
I have seen another poster on here say much the same thing.
On one hand I do get baffled when folk say they need to personally like a fictional character in order to enjoy a film or tv show, but I can understand more easily if they are turned off by a film they feel glorifies and can encourage certain types of criminal behaviour.
Also, some people just don't like going deep into the darker side of the human psyche with certain films, they just don't want to watch those types of character studies.
and maybe it's partly an aesthetic thing as well, I didn't like the Departed that much, whereas you obviously do, and maybe you didn't like Mean Streets that much, as you didn't rank it amongst his best, whereas I do. So even amongst Scorses fans there is disagreement and bemusement at opinions on his work.
edit: and as for the 'alien and incomprehensible' soundbite you typed up, well, it doesn't take much thought to ascertain that the people who hold these views may think that he's the type of guy who only has one string to his bow, and just goes for these extreme characters for shock value, or to keep attention away from the fact he does not have much of a story to tell.
Your a smart guy, right? I would expect you to try and understand where someone was coming from in this regard, unless of course, your letting your own personal fandom get in the way.