I use comments to verify things before I try to answer. I can see way one might want to limit new users from commenting: It prevent spam and unrelated comments, although it has disadvantages as it made me post "answers" that should have been comments. After a user has been active enough in a site, I think it's resonable and helpful to give him this privilege in all the sites.
For example, while I have enough reputation to comment on questions on Stack Overflow, I still cannot comment on questions in "Gaming." What's the advantage in that? It just prevents me from helping others.
(Maybe other privileges follow the same logic. For me, commenting is the one I miss the most.)