His works aren't usually explicitly criticized that often. More often, they're just ignored. Religious studies has become much more empirical, in that it now follows the conventional evidentiary standards of document based history and field work based anthropology. Eliade was in some ways the last to do grand theory like he does, trying to explain or analyze all of religion. His excesses, and the reorientation away from work like his, have meant that there were relatively few people in religious studies in his wake, and in many ways he was the last of a long line of people trying to understand religion as a general phenomenon, going back at least to people like Max Mueller, Emile Durkheim, Sigmund Freud, E. B. Taylor, and James Frazer. In a sense that people now treat religion as a contingent, socially constructed category, rather than a sui generis irreducible one, see the chapters "Religion as a Cultural System" by the anthropologist Clifford Geertz and "Religion, Religions, Religious" by J. Z. Smith, who was Eliade's dear friend and colleague and is probably the most important scholar for religious studies as a whole after Eliade. In many ways, Smith is Eliade's primary intellectual inheritor, though I think Ioan P. Culianu was being groomed for the task before he was murdered and others, like Mac Ricketts, have made a cottage industry out of carving out different little corners of Eliade's legacy. For more on Eliade and his reception, you should really check out Daniel L. Pals's Eight Theories of Religion, which is the absolute best book on all the major academic thinkers on religion in the through Geertz and Eliade.

The sort of grand theories of religion were avoided by scholars of religious studies for many years after Eliade's peak of influence. Only recently, with people like Bruce Lincoln's Holy Terrors and Theorizing Myth, Thomas A Tweed's Crossing and Dwelling, and Robert Bellah's Religion in Human Evolution have people started to once again approach religion generally. There may be some books from the 80's and 90's and 00's that I'm missing, but that Geertzian turn of looking at religion as part of culture rather than separate from it, looking at "powerful, pervasive and long-lasting moods and motivations" rather than "eruptions of the sacred into the profane", has had such a tremendous influence that Eliade doesn't even really need to be criticized by name. He writes almost like a theologian, rather than a historian or anthropologist, and while that's key to his appeal and lasting influence outside of the academy, it is also key to his marginalization within the academy.