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Glavine's final season in Atlanta, (first time), he went 18-11 with a 2.96 ERA.  His peripherals were solid normal (for him); 0.8/HR; 3.1-BB; 5.1-K.
Next season, at age 37, he's with a new regime and catcher.  He goes 9-14, 4.52 ERA (worst ERA since a rookie), and had a peripheral line of: 1.0; 3.2; 4.0.  The stock explanation was Glavine got old, and had "lost it".  Problem is ... he didn't.  His walk rate didn't budge, but his K-rate plunged to a career worst. 
In his next-to-last season with the Mets, (at age 40), he went 15-7 with a 3.82 ERA and a peripheral line of: 1.0; 2.8; 6.0.  Okay, you've gotta expect SOME variation over time.  But, he didn't miss a start in his entire tenure with the Mets. 
How to explain the massive swoon in his first season with the Mets?  Simply put, Glavine had pitched a certain way for his entire career.  The Mets had a different philosophy, and different defensive schemes and plans.  His pitching coach actually said in an interview the he didn't even TRY to get Glavine to change his approach for most of 2003, because he felt it would be either pointless or actively detrimental.  Instead, he WAITED for Glavine to become frustrated enough with results that he became WILLING to adapt.  He beat those 2003 numbers for the next 4 seasons, (even at age 41 -- barely).
Not blaming catcher - but emphasizing that the pitcher, catcher and defense ALL need to be on the same page to thrive.  And this is where CERA gets really problematic.  If a catcher has a disconnect with 1 pitcher, then the backup handles him -- no problem.  If he has a disconnect with two, but is really in tune with the ace, no CERA problem.  For a CERA problem to become visible, the catcher has to have a disconnect with the majority of his battery mates, (4 out of 5?).  THEN, the numbers emerge.
Joh doesn't mesh with Felix ... you adjust.  Joh doesn't mesh with Felix and Wash ... things get complex.  Joh doesn't mesh with Felix or Wash or Bedard or RRS ... now you've got a major problem that is showing up in results.  BUT ... maybe Joh DOESN'T have a problem with Snell and Fister and Vargas.  You 'might' swap out pitchers and see the CERA problems vanish ... and the conclusion?  CERA doesn't exist.  It was just luck or a standard abberation (sic).
Of course, the whole discussion is rife with pitfalls.  What if the pitcher is just losing it?  (aging, injured, in the midst of a divorce). 
The argument to dump Joh was never that Joh "couldn't" be a good catcher.  The argument was that the club couldn't swap out 5 pitchers "hoping" that Joh would mesh with them ... which is especially risky if you suspect that the root of the problem is cultural, not intellectual.