The main benefit MVD has over MDV is DHC to swords. If you’re like me and can’t do the TAC inf reliably, this gives you an easy TOD alternative. As mentioned, I still play it as MDV though, and am certain it is, at least as far as the game’s current theory, superior. Why?
-MDV has Vergil anchor. Mind blown? But really, that’s a pretty big benefit. I actually prefer Vergil w/ an assist personally, but I’d rather set that up via Sphere Flame xx Swords/DT or TAC or some swap-in as opposed to having Vergil come in and attempt to play neutral till assist is available. But more than all that, lvl 3 Vergil is, you know, perdy good. Plus, the later in the game Vergil has to deal with his own incoming, the less chance the opponent will be in a good position to spoil it, on avg.
-MDV doesn’t have Doom anchor (by default at least. My own antics sometimes negate this advantage, hehe).
-MDV has Doom 2nd as a TAC infinite engine. So whether you use it or not, Marvel theory dictates that is just WAY more of a tactical advantage than DHC to Swords.
-MDV will, in general, give Vergil more meter. Even w/o TAC stuff you’d still have 2 characters worth of battery. But WITH the TAC stuff, it’s just a mathematical landslide. And Vergil’s power is extremely proportional to his stocked meter.
-MDV allows for a strategy I call an ‘orbit’ strategy where I put my assist character in the 2-spot and hard tag from the 1-spot to the 3-spot and vice versa when one is badly bleeding, and would rather not go with the ‘just play them till they die’ approach (especially if they have a ton of red health left). Admittedly I do this mainly with Morri Doom Vergil, but the idea has the benefit of making it so if one point should happen to die, the character that then comes in isn’t the one still trying to recover red life.
side note 1: In case you ask the logical question: who are you, why should I do what YOU do? Chris G does this too, in fact I got the idea from watching him. I just decided to give it a name lol
side note 2: Raw tags in neutral are generally dangerous. We probably get away w/ it more often w/ Morrigan on point because she tends to litter the screen w/ bullshit first. And it’s still risky. So it’s possible this whole last MDV advantage isn’t really something you want to exploit too often. lol I still like having the option.
-MDV is the order in which virtually every pro who plays it runs it (CJ Showstoppa being the only oft-streamed exception I can think of off the top of my head). This isn’t to say you should blindly follow, and can’t blaze a trail, and all that fun stuff. BUT, since we’re talking theory here, you have to consider that these strong players just know what they’re doin’, you know?
There’s prob more, but I’m sure you’ve got the idea. Also note one neat thing about a game’s theory is that it changes. So if you like MVD, and even think it’s better, prove that shit! 
Yeah I’m not sure if theory dictates one is better than the other, but if it does, I bet it’s the beam (simply for the speed, ground control, and left right/stuff). But yeah, I too prefer to zone and just adore missiles-Vergil. Since both are so good for him, I usually just decide based on which my point prefers.