It’s technically the fault of the program, not the registry. But culture and ecosystems matter, and by-and-large, Config in files is usually much more concentrated.
2. Related to (1), it is very hard to just move settings from one machine to another. How do you export your settings related to program X in order to use it on another machine? I keep my Linux config files in a git repository - I can easily track history and clone it to new machines. What’s the registry equivalent?
3. It is incredibly slow. When I still used windows, if I needed to do some registry editing, I would dump it to a text file, edit and then import the edited keys. That took about 1/10 of the time doing the same took in ResEdit.
Meanwhile OS X or Linux don't suffer from this and working with applications is a lot more "streamlined". As I said, this is just a slightly above average skilled end-user perspective.