MoV means a player is rewarded based on how he played, not based on the difficulty of his games. I still thinks that a full win with a 115 MoV against a very good player is more valuable than a full win with a 200 MoV against an average player.
The difference between a full win and a modified win already gives a notion of how much the difference in points was. So this aspect is already reflected in the score. MoV only adds a layer in order to get rid of an unpopular SoS IMO. It also dictates players how they should play: more than 12 points difference is not enough anymore. This will affect how people will build and play their squadrons, resulting in less variety IMO.
My point is whatever the tiebreaker is, the pairing will always be a factor in the ranking, because that's how the swiss system works. SoS seems unfair to many players because you don't have control on your opponents score, but I think MoV is worse because it doesn't consider who you faced. Winning against a champion - no matter how you play - should be rewarded more than playing "well".