To be fair, the ending of season 3 was telegraphed even without creative interpretation. It's just that few believed they would actually pull the trigger on it and when they did they assumed it was Hasbro making them.
What upset me about s3 was simply that Meghan McCarthy is not that good of a writer, and not many in the writing staff picked up the slack. :/
What upset me the most about season 3 was that during seasons 1 and 2, it seemed like they were trying to build an actually believable and consistent fantasy world with some semblance of history. In season 1 in particular, every episode seemed to introduce some new aspect of pony society or Equestria as a whole or include details that practically cried out for more exposition. For example:
The Everfree Forest -> Why is it allowed to grow wild? The pilot hints that this wasn't always the case since the old royal castle is located there, but this question has never been revisited since.
Griffons -> Griffon the Brush-off introduced griffons as a sentient race and hinted that there is some interaction at least between pegasus ponies and griffons (Dash and Gilda going to the same flight camp). This raises all sorts of questions about what their society is like, what's their relationships with pony society, etc, but such questions have never been explored.
Ponies controlling the weather and the environment -> Pegasus ponies being in charge of the weather in Ponyville and the episodes Winter Wrap-up and Sonic Rainboom in particular drive in the idea that ponies are extensively controlling their environment. There would be ample room for exploring the concept further and introducing other ways in which ponies influence their surroundings but later episodes never go beyond depicting pegasus ponies controlling the weather.
I could go on but I'm running out of time here, so I'll just say that overall it seems to me that as the series progressed, the team got more and more complacent in simply reinforcing the ideas and concepts introduced in the early episodes instead of introducing new ones or trying to expand the world. In season three, we hardly saw any world-building at all beyond the Crystal Empire, and even that was quite poorly handled.