And this is where you're wrong. They just gained much more prominence, but back then, there were also tons of indie developers. The reason the indies gained so much more prominence over the last 15 years is because they continued making games with genres/themes that the publishers didn't want to touch anymore as they got more and more risk-averse. But that doesn't mean they just emerged back then, what changed is their visibility.
How many 90s indie games turned to be classics? I can't think any
Doom. Cave Story. Duke Nukem. Countless PC games that would spawn into big franchises. Just about every PC game in the 80s was indie and were sold at local shops in ziplock bags with dot matrix printed instructions on a 5 inch floppy.