Good points, however I think you might be leaving a few things out. The Diamondbacks have a much weaker lineup than the Yankees, so whenever you're bringing up which pitcher has the advantage, that should be taken into consideration as well.
In terms of the Diamondback's Series:
6/13: Hernandez has been good this year, but Mussina was really good in two of his last three starts, and the rain delay probably hurt him against the Red Sox. Mussina, if he has good stuff tonight, should be able to feast on the Diamondback's impatient, young hitters. The OBP's of a lot of their hitters speak for themselves. In my opinion, it is far from a "clear advantage".
6/14: This is pretty simple. Andy Pettitte is the Yankee's ace. Once again, "clear advantage" is going too far.
In general the D-Backs have a below average lineup, which I've already said, and that has got to factor into the equation.
In terms of the Met's Series:
6/15: Oliver Perez has been dominant at times, including against the Yankees earlier this year, however he is also inconsistent. Two starts ago he was nothing better than average against the Diamondbacks, and in his last start he was nothing short of poor against the Tigers. If the dominant Perez shows up then the Mets have a great chance to win, but that is certainly an if. On top of that, the Mets are struggling offensively right now, and the bottom of their order which consists of Jose Valentine, Carlos Gomez, and Julio Franco/David Newhan (or whoever DH's), is nothing to write home about.
6/16: I'll concede that your assessment here, or lack thereof, was right on cue, however you should remember that Glavine has not been so good as of late. Right now the Yankees are hitting better than the Mets, and if Glavine doesn't show up than it is far from a given.
6/17: I also agree with your assessment here. This is a toss up, plain and simple.