I tend to hang around here mostly, and we typically don't get into the kind of behaviors/discussions you're describing. I've seen that kind of discussion in other places, though.
For what it's worth, for as much around as I have been, I haven't commonly seen the CFM 'loids described as low-quality. I guess it might be a possibility for the older versions. But the impression I get is that, even if they don't all get equal time in the concerts, CFM takes care of their 6 synths, even going so far as to do sort of a backdoor update for Rin/Len (Yamaha required new software versions to be a new product, so they created a "new" version and mailed it to Rin/Len owners for free.) when they felt the initial versions weren't satisfactory. And, AFAIK, all 6 are moving to CFM's new engine together.
I don't know the context of the conversations you mentioned, but as one possible explanation, I'd suspect that low-quality is a description that should be thought of as having a very particular meaning. Maybe it means that the phoneme recordings were done under sub-par conditions. Maybe it means that the reclist was too small, so different sounds that are needed to sound smooth are missing. It shouldn't be anything in the software, since all Vocaloids should theoretically use the same engine....
What low-quality shouldn't mean is just general "didn't sound good to me." That's like saying that your favorite tomato sauce is Presto and Ragu is low-quality just because it doesn't suit your taste or meet your particular purpose. For example, if you're looking for a Vocaloid to speak native-sounding English, a CFM 'loid may not be for you, since English isn't the primary language for any of their VPs; even Luka, the member of the group whose English skills are most-lauded, requires a certain amount of care and tuning to do English well, IMO, because it's certainly possible to create a song where her English doesn't sound optimal. But difficulties with English shouldn't be a cause for a synth to be branded "low-quality," though I suspect that's one area where synths often catch a lot of flak.
Truth is, no synth by any company or on any engine is perfect at everything. They all have things they do well and things they do less-well or poorly. (For as much as any new synth or engine is often hailed as the best thing since sliced bread when it first comes out, after awhile of use people figure out that it has pluses and minuses, just like anything else.)
To get back to your other point, I think CFM's synths' popularity could have a lot to do with it, as well. It could also be that having a cute anime girl for a face or the voice types that many Cryptonloids represent don't appeal to some people--those things might not be ideal for particular uses, or may simply not appeal to some people.
Those are my somewhat rambling two cents, anyway.