I wholeheartedly agree. I'm sure the GUI works great for anyone used to it but it really is not logical, I simply can not count the times or frustrations I've had, going through each menu reading each item just to find that darn feature I was after.
Luckily they are redesigning the GUI for the next version, I'm hopeful that they will rearrange it as well (even though that will obviously be awkward for everyone already familiar with it) but I don't know, haven't paid attention to the development.
Case in point: Reboot, shutdown and Backup/Restore ought to be under the "System" menu, right? Nope. It's under Diagnostics, which is a large alphabetically sorted list (not by functionality or anything else, so if you are unsure of which term was used, well, you're better off consulting google).