No one was ready for Barry Lyndon when it came out in 1975. The filmmaking world was starting to lean towards directors like Altman and Coppola, both of whom would make films as long and detailed as Barry Lyndon (Nashville came out that years and was considered a masterpiece) but just didn't seem that way. Roger Ebert did treasure its greatness; it was one his candidates for the greatest films of all time.
By contrast, Eyes Wide Shut came out at a time when the world didn't want to go to those kinds of films anymore. It didn't help that the movie was released during the summer when everybody wanted to see The Matrix or The Sixth Sense. The era of the serious summer movie was pretty much dead by 1999, but I have a feeling even if it had come out in the fall, the reaction would've been the same. There would've been more attention for Kubrick's last film in some circles, but I think it would've gotten the same reaction. A shrug. Like far too much of Kubrick's work, it is only now being appreciated as the masterwork it is.