Gus Mueller writes about how these Lion features complicate workflows in his image editor Acorn.1 I had a similar problem when using Byword this month. After meetings I write meeting minutes. These follow roughly the same format: a Multimarkdown document with headings for Old Business, New Business, and other miscellany.
I never made a template so until Lion my workflow for things like this was to open a previous document, do a “Save As…” and edit the new document. With Byword in Lion, which includes Autosave and Versions support, “Save As…” disappeared.
I admit that the workflow is backwards, but anybody can see how scary it is for a user when they gradually learn they’ve unintentionally saved over documents they didn’t mean to save over.
As for the proper workflow, now I “Duplicate” the document, make edits, and when I want to Save, Byword offers to save it with a different filename.