I am going to take a stab at running the Mets at the deadline here.
I like to think of the role of the general manager as twofold: the first, and most important part, is to compile value (in terms of total WAR). The second, and more interesting part, is to convert value into wins, which is the "puzzle building" component of front office work. I tend to think that Minaya is very good at the second part, and simply does not think from the perspective of the first part.
But at this point, the Mets are probably on the fringe of having a store of value that could propel them into the playoffs, so we're into Minaya's territory right now (Minaya inherited a team with Jose Reyes and David Wright, and proceeded to added massive WAR infusions in Carlos Beltran and Johan Santana, but I don't think that he was thinking in terms of building the team's store of value as much as building a winner). The "puzzle" component of converting that value into wins leaves the Mets with three needed improvements:
1. The Mets need a starting pitcher, so that Takahashi can return to the bullpen, upgrading both sections.
2. The Mets need to upgrade second base; the Castillo/Tejada/Cora thing has been a disaster this year.
3. The Mets need to address their 3 catcher situation; the catchers aren't good enough to carry all of them.
1. Trade Barajas for a low-level prospect, PTBNL, or cash considerations.
I was one of those people who ripped the Mets for not kicking the can down the road when they decided to deal Ramon Castro and keep Omir Santos. Barajas, however, is no Castro, and Thole is no Santos (he's much, much better). The Mets should have dealt Barajas to Texas (as was suggested here) when he was hitting well; Texas ended up settling on cycle-hero Bengie Molina and probably would have happily given that package to the Mets for Barajas. (Texas dealt Chris Ray, a possible late season bullpen infusion, and Michael Main, a fringe minor leaguer, to nab Molina).
So, at this point, the Mets should deal Barajas. The return isn't important, but it's worth getting something. If they would rather not deal Barajas, then Thole has to be sent down. None of those catchers (Thole included) hits well enough to be worth a bench slot of a more defensively-versatile (or offensively-skilled) player.
Now, my WATPs:
2. Trade Reese Havens and Jeurys Familia for Rickie Weeks.
Weeks has mostly been a disappointment in his career, considering how highly he was touted when he first broke into the bigs. He has never played over 130 games in a season, and his career OPS+ falls at 103, which is rather pedestrian. This year, he's been healthy, though, and he's put up a friendly .270/.368/.447: nothing excellent, but not too shabby.
I'm not sure how much it would take to get Weeks, but on my count, he is a free agent after 2011. An optimistic valuation going forward has Weeks worth 6 WAR over that time period. More pessimistically, you could note that the highest value Weeks has ever had over a stretch of two seasons is 5.2 WAR. So reasonably, Weeks is worth between 4 and 6 WAR over the time period.
3. Trade Fernando Martinez and Dillon Gee for Ted Lilly
Lilly's price is inflated by his likely Type-A free agent status. Lilly is absolutely a rental; there is no conceivable reason you would ever want to re-sign him; your best bet would be to offer arbitration and hope he goes elsewhere.
I have no problem if people disagree with the amount of talent it would take to pick up these players; it is really hard to gauge how highly teams value their own players, and the prospects of other teams. But I think the players themselves are fairly realistic, attainable targets, based mainly on service time, age, and the expected cost-cutting of the Brewers. I also think they would represent a tangible improvement for the Mets, something on the order of 2-3 wins the rest of the way.
Lastly, a good second baseman would make Castillo redundant. The most disconcerting part of the roster, to me, is the lack of a guy who could realistically/desirably play third base, in case of an injury. I would have no issues DFAing Castillo under these circumstances and going to the scrapheap to find a more versatile back-up infielder, or to just bring up Nick Evans, if you are confident that he could fill in at 3rd in a pinch. You would have a very balanced bench going forward:
C - Henry Blanco
OF - Jeff Francoeur
2B/SS - Alex Cora
1B/3B/OF - Nick Evans
PH - Chris Carter