Here's what I think. I owned a Mark V for 5 years, a Mark V 25 for 2 years, a Dual Rect for 4 years, a Lonestar Special for 2 years, an Express 5:50 and 25 for 2 years, an Electradyne for 3 years, and a Roadster for 6 years. I owned some others, like a Mark IV and Mark IIC+ that I bought and sold along the way. I still use Mesa Black Shadow speakers in my main cab. Still, I don't consider myself a Mesa Boogie guy, and definitely no expert. However, I can tell you what the raw deal is.
First, when it comes to the Mark V, a lot of what you hear is basically opinionated crap as far as I'm concerned. When you say you can't get a good tone out of it, that raises some flags because it's hard not to get a good tone out of one. MOST of the time when people say that, it's because they had very particular expectations OR expected it to adapt to their particular instruments/speakers/etc. For example, if a guy is using high-output ceramic pickups, drop-tuned, and whatever effects, then plugs into a Mesa and dials the controls at 12:00, he's going to be very disappointed. Mesa Boogies do not have the same kind of tone network as a Marshall or Bogner. Plus, he'd be pushing the amp with powerful pickups and adding drives or effects and it's not all some easy plug & play deal.
The first thing you need to do it plug straight into he amp and dial in some basic sounds, then add everything else one by one - but to do this, you NEED to read the manual! I don't know how many times I heard the same jive only to find out they bough the amp and thought they'd take it home and hook it up like some generic amp as if it's supposed to output magnificent tone on demand. I don't care what amp you use, but if you take it home without considering the uniqueness of an amp's tone, design, and overall presentation, you're just setting yourself up for disappointment.
Metal players are some of the worst when it comes to this. I don't know how many times a Dual Rectifier guy, or Uberschall guy, or Mark IIC+ guy have come along and pissed on the Mark V only to find they had very specific preconceived ideas OR thought it logical to just generalize preconceived notions across amps. The vintage and purist guys are just as bad. I mean Mesa Boogies are not simple circuit amps, and Mesa Boogie amps in the past 2 decades are generally more modern sounding, with the exception of Electradyne, California Tweed, Fillmore, etc. Even those won't have such simple culircuits that you can actually hear the differences between certain brands of caps, etc.
Second, no one with a brain buys a Mark V expecting it to sound exactly like their 80's Mesa rig. No, that's not how it works. The Mark V has the exact amp circuits hardwired but it's still sharing other circuitry and a different global circuit design. You're definitely going to get authentic Mark IIc+ and Mark IV tone but it is a more modern amp and not going to be an exact tonal replica.
Another major stupidity with Mark V gossip has to do with not being able to 'click', or essentially settle with it. What you'll usually find with those guys is they never dial in a few good tones and just start using those tones like they would on a dual-channel amp. You have to find a few good tones, start using them regularly live, recording, and practice. When people don't do that, they lose sight of the amp's utility. It's like having a Swiss pocket knife. Most people use one or 2 blades most of the time, and occasionally the toothpick and scissors. You don't get a Swiss pocket knife and find regular utility for an entire variety of tasks every time you open it. Furthermore, everyone knows if you want a certain kind of knife, you don't buy a Swiss Army knife and expect it to do perfectly what that specific knife does well.
Therefore, a lot of it has to do with the mentality and expectations going into it; as well as what your guitars input to it, effects input through it, and speakers output from it. The fact is, the Mark V oozes great tone because it's an outstanding, quality amp. If someone has more trouble finding good tones from it rather than sorting out which tones they want to mainly use then something is wrong with how they approached it... and the same goes for many amps also.