I what way do you mean? The reg files are just one big .txt file basically. That is why it's slower for the OS to search through the bigger it gets.
Programs like "regedit" load the text file and arrange it so it looks like it's arranged more like your typical directory structure, but it's got no real directory structure of course.
No. The registry is stored as a hierarchical database. It's nothing at all like a big .txt file.
The main problem really is that there is no way for a person to clean it.
If a program installs keys like {58512179-5E5E-4431-B982-621CD856B1F9} and all the key values don't indicate what program it's from, how do I know if it is left over or something important?
There's generally no reason for a person to clean it.
