Yeah. I used to feel that way also. But since then I've changed my mind. Using middleclick is impossible to use if you want to perform a 'replace' on some text.
A simple example is try pasting a URL into your browser bar, at pretty much any point without opening a extra tag. Also many many times I'll lose my buffer by simply clicking on a terminal window and accidentally highlighting some whitespace or some tiny portion of text.
The advantage to the second buffer is mainly that you control when things are inserted. With a primary, traditional, X copy buffer it is often wiped out many times during the course of normal text manipulation in a GUI.
I wouldn't mind having 2 buffers at all except that how applications and X handles these buffers is broken. It's very inconsistent so you either have to learn how each and every application you typically use is going to behave, or you just end up having to copy stuff multiple times quite often.