I thought the same thing. I turned the bass down to about 9 o'clock still can get bass heavy and muddy real easy. I also am finding that with active pups it sounds really garbled. No clarity at all.
Even the clean channel doesn't clean up very well, I would expect with bright switch on and treble and mids up, it would be pretty clean and chimey, not the case. I tried it through my 4x12 and it sounds the same way. So, not just the 1x12 doing it.
I pulled the power tubes, and look like they are quite old, Tung-Sol 6L6GCs.
I may try changing V2 to something other than a Tung-Sol, this amp has all Tung-Sols in it, not sure that is good, as this is my first Mesa.