this is one of my biggest gripes with linux. I do prefer how it's done in windows. I don't like the fact that a package manager is required to handle programs normally, it feels convoluted and like it's meant to limit my control. Also, I keep getting different opinions on what goes where. like you said, usr, opt, bin, etc gets confusing and it feels like distinctions are arbitrary most of the time.
I found myself downloading program packages online rather than using a manager, extracting them to /opt and using them that way. it feels much better and I can just use an alias, for example seamonkey=/opt/internet/seamonkey/seamonkey or something like that, and it's all in one place.
on windows I like to organize all my programs into program files then into subfolders like communication tools, utilities, etc. One thing that is a problem here is program files (x86). why the fuck does it exist? 32 bit programs run on my 64 bit OS anyway, why should it matter? also, programs that refuse to install in a chosen directory and just install where they were programmed to are a pain, as are ones that refuse to have anything to do with paths with a space in them. it's just another character ffs.
on windows you also have appdata and all that junk. A lot of this crap comes from multi user stuff. fucking nobody needs multiple users on their system. only I use my computer. I think having a root or admin account for security is stupid too. Programs should only have access to the folder they're installed in, perhaps within the OS settings can be changed to allow it access to other areas or something. Seems like having an admin password, but not actually an admin user account would be better.
I think ideally after installing a system, you have a directory in which the OS keeps it's things and it can be organize however in there, and you don't touch anything in there unless you know what you're doing. and that's it. the user can do whatever else they want after that.
for example after installing linux it would be nice if all I see is a /sys or something, in which are all the necessary system files, and nothing else. then I can make /docs, /videos, whatever I want, and put programs where I want.
too bad I can't still use DOS.