Paper, supplement or what?

A reviewer just wrote in response to one of our papers

I am first concerned over the structure of this manuscript, being divided into what will be a printed article and an on-line supplement. The description of what I consider to be essential methods are fragmented across these two segments, making the article disjoint and difficult to follow.

I fully agree as I have the same problem with many Nature and Science papers. By the online evolution papers are even more difficult to read. Curiously, even PLoS does this split although there is no printed paper at all.
What about abandoning the supplement practice in favour of a full and an abbreviated version of an article? So we would have an abstract for quick screening, a brief version for the printed journal and a long, fully referenced online version, yea, yea.

Addendum 1-7-09

NG continues with this artificial setup

Starting this month, readers will notice a new section called Online Methods in our Letters, Articles and Technical Reports. Material previously published as Methods and Supplementary Methods is now combined, fully edited and hyperlinked in the new format that will be present on the journal’s website and reprints, and can be downloaded in PDF format. Readers of the monthly print journal will now be directed to find the Methods online.