Yesterday, in a game against a Cubs pitcher, Kyle Hendricks, who had given up 11 runs and 15 hits in his previous two starts (five innings each) and who entered the game with a 4.46 ERA, the Mets could only manage two singles and a double, scoring zero runs.
One of the Mets problems is the middle of the order, their 3-4-5 hitters. In the three-slot should be the team's best hitter. In that slot yesterday was Lucas Duda, who is batting only .260 with an ISO of .186, one fangraphs.com rates as slightly above average. But he is also striking out 22.7% (72) of his plate appearances or almost one in four. In the fourth-slot should be the team's best power hitter. Manning that slot yesterday was Daniel Murphy, hitting .282, but with an ISO of only .134, one fangraphs.com rates as below average, plus also below the National League average ISO for 2015 of .138. And in the fifth-slot was Michael Cuddyer, a player for whom the Mets sacrificed their 2015 first-round pick. He's hitting just .243 with an ISO of .122, which is also one fangraphs.com rates as below average. Worse, he has struck out in 23.7% (67) of his plate appearances and driven in just 28 runs in 72 games. In contrast, last season with the Rockies in just 49 games he drove in 31 runs and hit .332. Further, between Duda and Cuddyer, yesterday's #3 and #5 hitters, they have struck out 139 times.
In summary, one reason for the Mets weak offense has been the players batting in the third, fourth, and fifth slots.