Exiled from Continuity: Some people have...issues...with the Night Court, and the direction it was taking the Lunaverse. This extends to the series creator himself. While no Night Court story has been decanonized, RainbowDoubleDash has flatly refused to allow any more canon stories focused on the Night Court. The exception to this is TalonAndThorn's Climbing the Mountain series, for three reasons: First, it was already in-progress, and RainbowDoubleDash didn't want to cut off TalonAndThorn from finishing it; second, it is far more focused on showing a positive side to the Night Court, rather than constant scheming and dirty dealing (notably, our perspective character is the newly-created Baron Mounty Max and him learning the ropes and trying to improve things for his new province, rather than any political games focused on gaining power or gaining control of the Elements); and third, because it is considered "soft canon" that other "hard canon" fics can contradict and take priority over if need be.
Schedule Slip: 'At the Grand Galloping Gala', the season 1 finale, took over 4 months to finish.
Torch the Franchise and Run: Partial example; "At The Grand Galloping Gala" was designed to put an end to the Courtier plot for good. The massive backlash has probably derailed that.
What Could Have Been: As a shared universe, the series has plenty of examples, and Rainbow Double Dash and the other authors have revealed various deleted scenes and concepts they considered.
Before Cheerilee, Roseluck was originally considered as one of the Lunaverse bearers. RDD selected the Six before distributing Elements, with Trixie as Magic being the only one set in stone; if Roseluck had made the final cut, the others could've gotten different Elements as a result.
On a similar note, RRD has also stated that if Hurricane Fluttershy had aired before the Lunaverse was already being posted, it's likely that Flitter or Cloudchaser would've replaced Raindrops because of the potential of that built-in family dynamic. Probably for the best, since Raindrops is best pony.
Trixie was originally going to maintain her Third-Person Person tendencies, but as a habit she was trying to break.
Early on, Twilight was still going to have Spike for a companion; this would have been a double-edged sword, as he'd goad her into challenging Trixie, but Boast Busted wouldn't have ended so sadly. (Which could've effected the whole tone of the Lunaverse...)
During Longest Night, Longest Day, all of the Mane Six would've been shown to have been incapacitated during Corona's return.
In "Family Matters," for a brief period Fancy Pants was going to be Dinky's and Sparkler's father; however RDD chickened out and instead came up with the OC Castor Cut.
In the first draft of 'A Hard Bargain', Big Mac and Caramel were revealed to be employees of the Network, a combination of the A-Team and the Leverage crew who acted as vigilantes to fight evil and right great wrongs. This was later redacted for clashing with existing continuity (for instance, the Night Court would both know of and disallow such a group, and Trixie would report them as soon as she found out about them).