Off the top of my head, there are two major variables.
1) V30's vs C90's. The V30's have more of mid focus with lots of punch and can sound more bright/harsh if they're brand new, but the mellow out eventually. The C90's have a very rich high and low end, some how more dark and less in your face than a V30's (just my take on them).
2) Open back cab vs. closed back. All of the Mesa vert 2x12's and 4x12's are closed back. This helps with re-enforcing low end and making the sound more focus. Open back makes the sound mellower and well ...open sounding. You'll notice that in this regard Mesa chooses speakers that compliment the cab. V30 for closed, C90 for open.
I find it not to be a deal breaker in either case. If you play a lot of heavier stuff, closed back is ideal but not necessary. If I had my way I would have one of each speaker in my vertical 2x12. Keep in mind that in the 80's Mesa cabs were half open back, half closed and agree that a cab with both V30's and C90's, half open back is the best of both worlds. No matter what you go with, it will sound good.