EL34 run much hotter in Rectos, almost too hot for the silicon/bold setting (Mesa recommends tube rectification with EL34). So you are not only hearing the difference between the tube type, but also different bias settings.
For 2 channels I like 6L6 that run a bit hotter (code grey). For a 3 channel 2000-2009 I maybe would try EL34 as the amp has extended lows and highs. For the MW again 6L6.