I think the 'balance of usability' would be perfectly easily defined by the end-user more than the programmer.
How about making the OS scalably responsive based on how it's used? "Gee, this guy only seems to use notepad and Firefox, and he has a hard time reading the text because he keeps enlarging it. Let's do that for him, and keep Notepad at the ready. Maybe even in a few weeks archive some of his least-used programs and data files to save system space. But make sure he knows we'd like to do it, and give him the option to decide not to."
"It looks like this guy really likes to play DX games and surf the web, and tweak his configurations. Let's give him the option of enabling administrative mode more easily and seeing hidden files, but allow him to disable it if he ever wants. And while we're at it, let's prioritize DirectX applications when they're running fullscreen so he gets the best experience out of it. In fact, he's so good at using this thing, let's let him have the option to modify his resolution, UI features, button sizes, text and color formatting, refresh rate, even tinker with his registry. He obviously knows how to handle it."
"This person thinks they know what they're doing, but they changed something that we had to adjust to make the system functional again. If he tries it again, we can just give him a polite reminder of what happened last time and offer that he seek support on the subject on our forums before he continue enforcing the same changes as before."
And most importantly...
"This person really doesn't seem to like it when we augment the OS's actions based on what they do, so let's just disable it and let him change his ability to access things manually."
All you have to do is make sure that the OS lets the end-user know 'Yes, we did this, and no, it wasn't a virus. Do you want us to put it back the way it was?' Give the end-user all the options but also the protections for the people who think they know what they're doing or the ones who DO want to minimize it for their use to a handful of actions.
I'd even be happy with after two months it goes 'You have a bunch of programs you never ever use. They're components of the OS, but if you never expect to use them we could remove them for you. Would you like to see a list and take out things you don't want to improve disk space and possibly even system performance?'
And last but not least, have all these annoying questions and thoughts in a convenient little place that doesn't get in the way. Popups on the taskbar? Maybe. But better yet, how about a scrolling ticker on the desktop? It floats behind other objects/windows, asks questions about your system use, and can also be configured to constantly inform you of important things. From RSS feeds to the weather, if you have new email, or occasionally mention your system performance.