“They kind of have to kind to convince me,” Manuel said. “Because I believe a guy should learn how to pitch. The more he gets out there, the better pitcher he’s going to become for you.”
“Because if you’ve got a guy pitching well, and you’re trying to win games, then that puts some shackles on you,” Manuel said. “That’s tough. What if a guy’s throwing a no-hitter?”
“I don’t have any problems with the dialogue or what have you,” he said. “If the majority feels that [he should be limited], and proves that this is going to make something better for whatever, I don’t see a problem with that.” Source: NJ.com
I happen to still like Manuel, and that was a reasonable argument made at a time when it made sense. A dialogue is good, and you might want to use your instinct and senses in addition to looking at a strict numerical pattern - especially considering Niese has hurled around 180 innings in a season before (in 2008).
But that was a week and a half ago, and things have changed since then. With Niese now over 150 innings in a lost season, it is time to skip a start or shut him down entirely. Although he had a longer season in 2008 (124.1 IP in AA, 39.2 IP in AAA, 14 IP in majors), he had an injury-shortened season last year, only finishing 120 frames.
A few days after the above quotes were issued, Manuel made another comment regarding young Niese. Asked again about the innings limit, he said:
"We touch on that kind of stuff all the time, but we haven't really sat down and put anything in ink," Manuel said. "I think a lot depends on if we see a diminished product, if we see fatigue. Then I think we'll probably visit it with some sincerity." Source: MLB.com, via Mets360
A dialogue is worthwhile? Fatigue is the key? Well, now is the time. Niese has been lit up in each of his last two starts. His last start against the Marlins was his second-worst of the year, as he surrendered 7 earned runs (season worst), and threw 43 balls (third worst). His only start worse than that was tonight against the Braves, as he allowed eight runs (only three earned) and got knocked out in the fifth inning.
Another interesting data point is how Niese has appeared to wear down during the course of both games. In tonight's start against the Braves, Niese held the Braves scoreless through three innings, before surrendering one run in the fourth and then seven runs in the fateful fifth inning. This is similar to the start against the Marlins, when Niese had only allowed two runs and struck out seven batters through five innings.
Niese has been wonderful this season, but he's now had two horrendous starts in a row. In both starts, he was uncharacteristically wild and was completely hammered after the fourth inning. He's showing big time fatigue. He's over 30 innings in excess of his workload from last year in a season which is completely lost.
For what it's worth, many believe that 30 innings is the magic number for young pitchers, and that an increase in workload in excess of that exposes them for a risk of injury. A quick definition of this, called the Verducci Effect by some, can be found at Baseball Prospectus:
Named for Tom Verducci of Sports Illustrated, this is a negative forward indicator for pitcher workload. Verducci, who called this the 'Year After Effect,' found that pitchers under the age of 25 who have 30-inning increases year over year tend to underperform. Will Carroll independently found that pitchers who break the "Rule of 30" tend to get injured. Carroll renamed this 'rule' the Verducci Effect in honor of the man who initially found the evidence.
The "Effect" makes perfect sense, but I'm not going to tether myself to a super strict mathematical pattern. In the end, each pitcher is an individual - an individual employed in a profession which the human body was never intended to perform. At the end of the day, it may not matter what kind of precautions you take, whether super conservative (i.e. Strasburg, Stephen) or otherwise (i.e. Ryan, Nolan).
In this case, though, it's time to shut him down. The development of Jon Niese might be the single greatest thing to happen to the Mets this season, and there's no reason to risk him further.
 It is relevant to note that the injury was not pitching-related, per se, as it was his hamstring and not a shoulder or elbow, but the effect - reduced innings - remains the same.