The human brain doesn't have any problem interpreting non-flat icons, as it doesn't have any problem with real world objects. We didn't have that problem you're saying before the flat design trend. Also icons should be aesthetically pleasing. When I see a iOS 6 homescreen, I see something beautiful. Can't say the same about iOS today.

And I'm going to stop here, because people are going to downvote the hell out of me. Design can be something very divisive.