Broken Base: The Ending of Silent Ponyville 3 was not received well, and even the writer himself said he had bit off more than he could chew and wasn't really happy with it, and wasn't sure if he even could've ended it in a way he was happy with due to how things played out. Mainly caused by Spike being Killed Off for Real and Twilight growing to hate Celestia after finding out she's a Retired Monster
This seems to be at least somewhat improved with the True Ending of Silent Ponyville 3, giving overall a better narrative and a more appropriate response for Twilight. More fans were happy or at least satisfied with its resolution, shame it took 3 years to appear. Also, Spike's still dead, but Twilight gets closure at least.
Creator Backlash: Sam Rose is not proud of Silent Ponyville 3 due to how weak it is compared to the last two incarnations and especially with the heavy fan reaction to it and is actually one of the reasons he hasn't had any ideas for continuing the series towards the reactions to Silent Hills. The reactions to the only finished ending were a big factor because even he agreed he did a horrible job wrapping it up and wasn't sure if he could actually reign in the large scope of the story to a satisfying conclusion.
The Creator, Sam Rose, however has more recently seemed perhaps interested in bringing the series back, if Readable Teaser is any inclination.