I don't think Mary Sue is a meaningless term, but that there are people who misuse it. I mean, yeah, if I see a Harry Potter fanfic (to give an example of fandom where I've seen a lot of Sues) where an OC is smarter than Hermione, the perfect Quidditch player, and has every person of their preferred sex falling head-over-heels for them, I think it's fair to call that character a Sue. But I agree that it's more important to address why these characters are dull for people who are not the writer to read about, even if they do actually qualify. (Part of the problem is that with those checklists, any original fiction protagonist who is the most specialest in their world in some way - e.g. Harry Potter, Edward Elric, Buffy Summers - is going to qualify. And people don't understand why this doesn't quite work for fanfic.) The main issue with 99% of actual Mary Sues is they're basically about wish fulfillment for the author, and so if you're not the author. that's not your wish fulfillment and so it's boring and you can't relate to it. It's the same reason no one wants to hear about what someone else dreamed about last night.
Anyway, the main differences between constructive and non-constructive criticism: a) Tone and b) Are you actually giving them any tips for how to improve their work?