I love Mesa amps, having owned/own 6, but never a Mark series, unless you count the Tri Axis. They can be hard to dial in, but once you do, they sound amazing. You have to ignore where the dials may end up, and rely on your ears. If the Bass wants to be on/near 0 to give you the tone you want with your guitar, then so be it. I've also found you have to keep going back to other settings, and re-adjust them, once you've adjusted others. It took me a long time to get tones I really liked out of my DR and Tri Axis, but it was worth it, in part because it taught me how Mesa's gain staging works. And I've read several of their manuals, many times, which also helped. I don't like that they're this complex, but I understand why.
As for the amps in the Axe, jeez, there's so many good ones, that if I can't seem to get what I'm looking for in, for example, the IIC+, which I have tried, I just move onto another one. So far, I like the Triple Crest and the JPIIC the best. Modern rock crunch tones using a Majesty.
As to the "mystique" surrounding the IIC+, I'll venture a guess: It was John Petrucci's favorite amp early in his career, his ungodly chops made many guitarists take note, and of course, they wanted his tone, so they started with using similar gear. He got an endorsement from Mesa Boogie, and used many of their other amps, but always seemed to gravitate back to the C+, which further reinforced the throngs of guitarists wanting to play like him (I'm one), which only furthered the desire of the amp. Then, he got a signature amp, and what's his favorite part? The IIC+ circuitry.
And you've also got Metallica that have used them, so there's that also.