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Nothing's wrong with linked replies per se, except that if a lot of replies are made to replies of replies, then things start getting really unmanageable. This is why, if linked replies are going to be implemented, a thread view needs to be implemented too. I'd say it's either all or nothing: optional thread view or back to the old way with no linked replies, but just plain linked replies are a pain in the ars, in my experience.
Now that I think about it, Gadrel's right: linked replies do encourage people to nitpick instead of filtering their thoughts for the maximum effect. Unfortunately, I don't think there's any going back at this point.