Zecora and Cheerilee
Probably because once you add the details that turn a stock character into rounded character, you’re basically stuck with those details. If it wasn’t broke, they saw no reason to fix it. I would imagine that as more time went on, new writers were less eager to tamper with the “Faust Era Stuff”.
Cadence and Shining Armor
You can blame the writer of “The Crystal Empire” for that one. That would have been the time to flesh them out more, but most of the stuff in that episode is woefully underdeveloped.
after the M6 had largely achieved their series-long goals
I really need to do a huge writeup on the structure of Season One. To make a long story short, Twilight has her arc in the pilot, where she learns the value of friendship. Beyond that, The Mane Six learn lessons, but they don’t fundamentally change as characters over the course of Season One. Instead, the audience’s perception of them changes as we gain a more nuanced understand of them. That way, they could have all accomplished their goals in “Best Night Ever”, and we the audience would have gone
“Well of course they accomplished their goals. These ponies are awesome.”
But that didn’t happen. When The Mane Six finally accomplished their goals, it wasn’t the culmination of anything. It just arbitrarily happened one day. I think it’s fair to say that G4 needed a new narrative throughline after Return of Harmony, regardless of what direction fans wanted the show to go.