Jan,
I found out that the 3-bath kit is only truly E6-compatible, if you process film of the same brand a time. Mixing e.g. Fuji and Kodak causes a slight magenta cast on the Kodak film. This is not the case with the 6-bath process. So as long as you don't mix brands, the 3-bath process will be as good as the 6-bath one.