Here's a simple exercise - look at the pre-season projections for everyone who's played for the Mets, multiply by how much they've actually played, and see how many runs we should've reasonably expected this team to score and give up.
For hitters, I took the PECOTA projection of EqA (which is a measure of overall offensive value), looked at the actual number of PA for every hitter who has played for the Mets this year, and then made a small adjustment for the park factor. According to the pre-season projections, the Mets should've scored 324 runs so far this year.
For pitchers, I took the PECOTA projection for ERA for each pitcher and then multiplied by their actual IP to determine how many earned runs the team was projected to allow. Since PECOTA doesn't project unearned runs, I assumed an average number of unearned runs for the team as a whole (the average MLB team has given up 26 unearned runs this year). The PECOTA projections come out to 332 total runs allowed.
Here's a table comparing the PECOTA projections to the actual performance of the team this year:
The Mets have been slightly better on offense than projected and slightly worse on pitching/defense, and pretty much the same if you combine the two.
So, blame Omar for putting together a crappy team. Blame the trainers for failing to keep the team healthy. But, it's hard to blame Manuel and the coaching staff for failing to get adequate performance from the players they've been dealt.