If conversations aren't nested, how are you supposed to know what the replies are referencing? There's no effective way to talk to each other and have a real discussion.

All of the 'problems' of nested comments are trivial in comparison to that. There are certainly good use cases for flat comments, and I think Stack Overflow is a good example, but there is a reason why all of the biggest discussion sites use nested comments. There might be more sites with flat comments overall, but that's only because they're much easier to implement.