A few more thoughts on this ...
At least from my experience, neither of the amps you mention are ever really going to deliver the goods until you crank the volume past 5 or 6. Which is likely to get you evicted or arrested, depending on your living situation.
Assuming that this isn't an issue, the next thing you should be looking at are the power tubes ... followed by the speakers, as you alluded to.
A pair of vintage 30s have the capability of delivering a very smooth tone, even at very high gains and volume levels ... while remaining clean and upfront. Similarly, I tend to favor EL34 power tubes whenever possible ... if your goal is to have the whole smooth hi-midrange thing. 6L6s might give you a more modern tone, but have that capability of ripping your ears off in the right situation.
I guess the moral is to be very thoughtful in your selection of tubes and speakers, because they will have an enormous effect on the sound.
At the proper volumes (read: loud) ... and with the proper tweaking, there is no reason why you shouldn't be able to get a very good sound out of either of the amps at your disposal. Granted, I would certainly tend to favor the 2000 for more of a classic rock tone, and the Mesa for a more modern thrashy kinda' thing ... but between the two, you should have your bases covered, again with the proper tweaking.
If all else fails, find someone in your area -- a professional technician -- who modifies amps, and tell him what kind of tone you're looking for, and solicit his opinion and see if there's anything he can do for you. Keep in mind that most of the really good recorded guitar tones in history have come from heavily tweaked amps.

That's just the way it is.
What I found myself doing at one point in time was watching a lot of local live acts, and when I heard a guitar tone I really liked, I would wait until after the show and ask the guitar player how he got it ... and usually they would throw out the name of a local technician who helped them tweak it or whatever. It's very common.
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