It is no longer 2004. Manny Ramirez is a an aging, defensively challenged, injury-prone defensive liability whose trends are definitely downward. He takes at-bats off. He takes games off with phantom injuries. He's expensive, and for all the "Manny takes hitting very seriously" stories we got earlier in the summer, he's quite clearly a pain in the ass. When Peter Gammons throws you under the bus, you've been very, very naughty.
Meanwhile, in Jason Bay, the Red Sox get a guy who is younger, cheaper, under their control for another year, and in the same neighborhood as Manny's level of production. Oh, and he knows what that big leather thing on his hand is for when he stands out in the outfield. Is he, at his best, the player Manny was when he was at his best? No, but Manny's never going to be that guy again, not unless it turns out he's from Gallifrey.
So, really, any analysis of this trade that overlooks the fact that Manny is now 36 and injury-prone is kind of missing the point, and ultimately irrelevant. The Red Sox gave up a couple of semi-prospects they were never going to use and some cash, which they've got plenty of, for a better outfield solution that gives the good production at the plate, another year of certainty as to his status, fewer Scott Boras shenanigns, and most likely lower psychiatric bills for the aging travel secretary Manny shoved a few months back.
In other words, it would have been find to rend your garments over the deal if this had been made in, say, 2003. But it wasn't. It was made in 2008, and Manny is a fading, injury prone lump and a distraction, and getting a guy as good as Jason Bay for him says this trade was a winner.