Files are terrible in all versions of Windows. Lots of developers have tried figuring out the best way to allow programs to have access to it's files but not clutter things. Linux had a good one for a while when they hid everything in an invisible layer, but I haven't seen that in years.
Apple has the best right now where "programs" are actually specialized folders that have everything that the program needs. Programs don't make any files outside of that package with the exception of documents. That makes drag and drop installation and removal instead of having to go through that stupid Windows Install Wizard.
Microsoft has had that Program Files folder for 15 years, it's time that they got rid of it.
Oh oh, even worse than Program files... has anyone ever written an app for the Solaris OS? *shutters*