I think one of the main reasons behind S3's weaknesses is a certain writer. No, not the much-maligned Merriwether Williams (although I thought Spike at Your Service was the second-worst episode of S3), but, in fact, Corey Powell. Furthermore, upon further thought, Sleepless in Ponyville was absolutely dreadful - the worst of S3, in my opinion.
Here's why I feel this way about Powell and SiP:
- Scootaloo-centric and heavily featuring Luna episode = way-too-obvious fanservice. Although Magic Duel could be counted as such, if I'm not mistaken, Larson once tweeted that when he wrote Magic Duel, he was not cognizant of the cult-like following that Trixie had built up within the fandom. Corey Powell, on the other hand, was a new writer, and, as such, likely knew of the high demand for a Scootalove episode, as well as the fandom's adulation of Luna, and wrote an episode combining the two.
- Even in the case of Magic Duel, even if it was blatant fanservice, there was a purpose to the episode - to provide closure on the Trixie arc (and remember, it was hinted at in Ponyville Confidential). Sleepless in Ponyville, in my opinion, was 100% fanservice and nothing else.
- At the very least, Merriwether followed up MMDW with the excellent Hearth's Warming Eve and the outstanding Putting Your Hoof Down, both of which showed brave, ballsy writing on her part, particularly the latter. Powell followed up SiP with... the bland, safe, lackluster Just for Sidekicks. She strikes me as a writer who's just "going through the motions".
That's not to say that other writers weren't culpable for S3's being weaker than S1/S2, but I think the addition of Corey Powell actually weakened the writing panel. I'm also inclined to agree with you in that "they wanted to hit the 64 episode mark more than they did want to make good episodes" - it definitely seems that way.
I'll make my pre-season grade prediction now:
MLP:FiM S4 will be a D+ and jump the shark.
Regarding the Spongebob movie:
Many fans consider the Spongebob movie to be the last high-quality production by Hillenburg and company, although I actually quite like S4. I do agree with you that Seasonal Rot was setting in well before the movie, though. However, I don't think Spongebob fully jumped the shark until the dreadful Season 5.
The comparison with the Simpsons is quite apt - it, too, jumped the shark around its fifth season. Disappointingly, Groening and his team haven't recognized this, and it's now on S25. :(
Where I live, they're broadcasting S23 of the Simpsons. I recently watched one of its episodes, and, my God, it was fucking terrible. It hasn't just jumped the shark - it put on a goddamn Superman cape and soared over the shark.
Also, Debbie Downer, Negative Nelly - take your pick. XD
P.S. I think that we can say that Spongebob quite literally jumped the shark.