The difference is that the automatic numbering is lost. It's a serious difference, in that it pretty much ensures that people will stop using that notation.
If we don't think the numbered url references are useful, then it's fine that it's being lost.
Yes, that's pretty much the issue I agree. From my point of view, it's good riddance. I didn't much like the feature (I think every link should be described in place), so I have no problem getting rid of it. But if there are lots of other people who think it's the greatest thing since sliced bread and can convince me that it's vitally needed for something, then I'll reconsider.