I can see what you're saying, but think about it this way:
The Yankees had 2 weaknesses last October: The Rotation, and the Bullpen. They've improved BOTH of those areas:
Johnson > Vazquez
Pavano > Lieber
Wright = Loaiza
Rodriguez > Proctor
Stanton > Heredia
The Red Sox won the World Series, so you can't say they were weak, but I'd say the bullpen was the biggest weakness. They lost Myers, Williamson, Mendoza, and Adams.... Williamson when healthy was NASTY, but he unfortunately didn't contribute a whole lot to the team last year, and certainly not in October.
Myers was replaced with Halama. Neither one is really dominant, so I'm gunna call this equal.
Williamson was replaced with Mantei. Equal again. Both are dominant relievers when healthy, but Mantei is certainly no guarantee.
So, in my book, the Yankees have improved this offseason, and the Red Sox have basically stayed the same. I like the rotation because it's deeper, but ONE of the 3 newcomers (Clement, Wells, Miller) needs to step up and take that #2 spot before I consider the rotation BETTER than 2004.
I give NY the offseason edge for that reason.