I tested Unicolor E6 six bath versus three bath when the three bath came out and actually preferred, very slightly, the results from the three bath. But that was so long ago I couldn't tell you any more about why, just that I settled on the three bath. I didn't have any visible problems with it, and went through a couple of one gallon kits back when I was doing E6.
Weren't there concerns about the permanence of film developed in the three bath stuff versus six? I can't say anything about that. I have some slides from those days which look ok (and none that seem badly faded as far as I recall, but I don't have all of them by any stretch) but I didn't mark them as to which process I used so now I've no idea which are which.