I dunno from experience (I don't have an invite) how the VT compares, but what "sells" MapTool to me is the drag-and-drop mapping. There's a 2-gig image repository of tokens and mapping images that they have distributed, and being able to plop down any old picture and use it as a map is a great feature that allows me to use things like online random mapping software and Google Image Search while drawing lines to design my dungeons.
Macros and library tokens also come in handy. I'm no coder, but the community over there does AMAZING things that help all sorts of games run very, very smoothly.
The lack of Voice doesn't phase me much, since Voxli does the job admirably and for free. No voice-changers, but those won't sell me a thing.
The pain of it is that it's a hassle to add in stats for everything. Since MT isn't run by WotC, you've gotta hand-add in everything. Now, the Compendium helps with copypasta, and I would not be surprised if a parser doesn't exist to help quickly add in things from a Character Builder file, that's certainly not one of the major focuses of the community.
It's also sort of catch-as-catch-can when arranging a group. Visiting random message boards and hoping for the best.
WotC certainly has the possibility to vastly improve on BOTH of these. Being THE website for D&D makes the community obviously interested in gaming, and being able to interface with the CB and Adventure Tools should make adding creatures and characters a simple thing.
From what I understand, the mapping isn't quite to the MapTool level at the moment, and there's no macro automation.
The two products seem like they might be competitive, that each has give and take.
What edges out MapTool at the moment is that it's free. The minor hassles are enough to deal with when the group doesn't need to invest $1 in anything extra.
WotC needs to compete with free.
The higher they make a group's entry price ($10 for the DM to have a sub? $60 for everyone to have a sub? free for anyone, but DDI for integration?), the less it will be able to compete, and the more MT's minor failings won't seem so bad, especially given the edges they have.
But, anyway, that's something for the project directors and upper management to fiddle out. That's why I've got some lingering trepidation. I trust the low-level folks at WotC fairly broadly. It's the upper-level direction that sometimes seems completely narmed to me. It's entirely possible some manager somewhere looks at a possible $60/month group buy-in, and hasn't heard of MapTool, so doesn't think that there's any real competition. That would be a mistake, I feel. But they could also be good at their job and entirely aware that they need to compete with a very solid free program.
Time will tell!