Everyone is up in arms about a feature change. This article at Read Write Web by Marshall Kirkpatrick explains what's going on and this comment really clarifies things. (Give the comment part of the page a few seconds to load).
First of all, I didn't realize the difference between a reply on Twitter where the @userid appears at the beginning of the tweet, e.g.,
@otherguy I absolutely agree with you!
and a mention on Twitter, where the @userid appears somewhere else in the Tweet.
I have to say that @otherguy seems to have a handle on this.
It seems all of the brouhaha is over replies appearing on your home page.
As the above articles point out, this is a feature that I don't think I ever had turned on in the first place and I was already confused about why I wasn't seeing replies on my Twitter home page.
I had sort of punted and was relying on Twitter Search to find posts and replies, but that is a more awkward, per-user-target type of approach.
Why they would remove a feature that only 2% of their users have turned on in the first place, at the cost of such an uproar (even if it's misplaced) is unclear to me. At least a lot of us are learning more about how to use Twitter in the first place.