I can think of two big ones off the top of my head:
1. Speed - some portions of the registry may me accessed thousands of times a minute.
2. Security - forcing access through a controled api allows ACLs to be use in ways that would be really messy to replicated in flat text files
Just think of all they reasons why you would move from a flat text file to a 'real' database and chances are they will apply.
At some point the sum of these advantages overcame the advantages (simplicity/human-readability) of ini/config files.
BTW, no one if forcing the use of the registry for everything. There are still plenty uses for ini/config files.