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As others will no doubt tell you, this is common complaint of new users. Because calibre is cross platform, there are limits what can be done with the user interface. Optimizing for Windows makes it less useful on other platforms such as Linux or Mac.
There is also little consensus as to just how it ought to be reorganized, since it is used in many different ways by its different users. Being a Sony guy, you could throw everything non-Sony overboard as for as I'm concerned, but Kindle users, which are a large number of users, would feel differently.
Kovid Goyal, the creator of Calibre, accepts contributions of code, since it is open source. You are free to try to try to re-write the interface code if you have the ability and inclination. He of course has to evaluate any contributions to make sure they will not create new problems and new support headaches for him.
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