> That, in itself, can be kind of annoying
Of course, but is it more annoying than using Windows all the time? OP leads me to belive a growing number of windows users might think otherwise. It's also worth noting that rebooting is an order of magnitude faster than it was 10 years ago.
> having to run updates for both
Updates are a pain in Windows, but they are not in any serious GNU/Linux distro I have ever used. This is one of the main reasons that users are frustrated with Windows in the first place.
> having two incompatible filesystems where it's annoying to fetch a document from one and use it on the other
This is a real problem when you are using Windows, but not when you are using Linux. The idea here is to only use Windows when you need it anyway. It's an inconvenience, sure, but is it more of an inconvenience than using Windows all the time? That's up to the user. Personally, the answer is no.
> doubling the amount of setup and configuration you have to do
Not so much, if you seriously use GNU/Linux for everything you don't need Windows for. Besides, configuration isn't a big issue unless you are like me, and want everything exactly your way; although, GNU/Linux is the only way I can get that.
> Every time I've set up a dual-boot system I've ended up just never using one of the options.
That's you, and that's fine. The best setup for you is almost definitely not the best setup for most other people. That is the entire reason to use and promote free software: liberty.
Windows has made dual-booting difficult on purpose, because proprietary software begets proprietary software and control. Thankfully, there has been plenty of work in the other direction for those of us who want to control our computers, as opposed to the inverse.