It's unclear to me if the Twins decided that they had to get Johan Santana out of the AL, or if the Red Sox and Yankees had gotten fed up with the process and decided to either keep their young talent or replace the frontline members of the trade with other prospects, but the players the Twins are getting from the Mets (Carlos Gomez, Deolis Guerra, Philip Humber and Kevin Mulvey) are just not good enough for a pitcher of Santana's caliber, i.e. the best pitcher in baseball at this point. As Jim Callis, editor of Baseball America, states in this post, "Guerra and Gomez come with high ceilings but also lack a lot of polish and have a long ways to go to reach their potential. The odds that they both will do so are slim." He also projects the two other pitchers as #4 starters on a major league team.
Baseball Prospectus projects Santana as a Met to finish the year with a 2.94 ERA and 239 strikeouts. For reference, Jake Peavy led the majors in strikeouts in 2007 with 240. Scott Kazmir led the AL with 239. Only Peavy would have had a lower ERA in 2007, finishing with a 2.54 mark. This immediately gives credence to a Mets rotation which now includes Santana, Pedro Martinez, John Maine, Orlando Hernandez, and Oliver Perez. The Mets are hoping that Maine, Hernandez, and Perez can all provide the types of performances they gave the Mets last season, but there is cause for concern for all three. Maine will be entering his second full season as a frontline starter, giving opponents a better chance to look at him, and Hernandez and Perez are known more for their inconsistency from year to year than their effectiveness. Nonetheless, combined with the punch that the New York offense provides, the Mets have made themselves the favorites of the NL East with this trade (regardless of what the Braves would have you believe - "Santana deal brings parity to NL East").
Edit: Ryan pointed me to this article by Aaron Gleeman, a writer for Rotoworld. In it he tempers the Twins hating, and provides some hope for Minnesota fans in addition to attempting to rationalize Bill Smith's decision.