I've played a bit of both, so here's the differences.
* There's no real way to respond on another player's turn, which lessens the strategy, but also means you're not waiting on your effects to resolve forever. Games generally take much less time (~15 minutes at most)
* Not quite as chancy. You just can't win on turn 3. The infinite and quasi-infinite combos of MTG are, as of yet, nonexistant. And there are some *good* combos, but you can't base your deck on channel/fireball as you could during MTG alphas;)
* Harder to keep permanents. All permanents are characters or attached to characters which can be damaged directly via attacking them with your creatures. As a result, utility creatures are much harder to keep alive.
Blizzard's done a great job of making a CCG that actually plays well online by designing it to be that way from the ground up. Unless MTG does a redesign, or at least designs cards specifically to be played online, it will always be a cludgy using a Windows Tablet circa 1999 (or a Windows 8 machine circa now).