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> I will make Pinkie Pie with that sax an air defense unit; look at what she did to that bird and the fact that she managed to disorient even the wonderbolts.
and the fandom laughs at earth pony magic....she didn´t have these powers in Swarm of the Century but behold to this seemingly innocent pony. The enemies better not have any air instruments at sight.

> Though she did cause things on the groud some pain and caused apples to explode her most impressive feats where in the air.
and she could perfectly cause things in the sea as well, she didn´t step into the zone fortunately. Air, earth and sea are not free of what she can do. They´d better not laugh at earth ponies and much less Pinkie Pie, the one who you cannot question her actions.

> It will be interesting to see if they address this in the show
> It'd be cool to me if they do and specifically call back to this episode too(even cooler, though unlikely, if they sprinkled tiny hints in a few other ones before they addressed it)
it is actually fairly unlikely to happen. They could mention what she has done with the yaks but not the way we are imagining (sadly). Unless they make a punch on the table like Larson did with Amending Fences, an average writer doesn´t usually go that far in terms of emotion or passion. This is why the fandom doesn´t have high expectations because they don´t go much further (despite that the show has gone beyond the initial concepts).
The correlation between Pinkie and the yaks is almost definitive but your petition is pretty unpopular because the yaks barely bring any interesting for the fandom´s eyes, only Yona is well liked.  But again, dreaming about it is free for anyone and it would be nice if it actually happened. 

> It almost gives me a tiny bit of a haunting feel to when it is put in that context. 
definitely.

> I have a hard time giving something a rating because I often get lost on what measures I should judge it. 
You have mentioned this in the past with my two latest fics and yes, I am not that fan of ratings either. They are more like a reference in order to set the expectations or views on it but not enough to describe the complete thoughts on it.  I prefer the observations as well or certain comments. 

There are "professionals" out there that rate something with the first contact and masterfully have a view on it, leaving it behind without looking back. Music reviewers are like this and a few years later, they suddenly reconsider their views. In this fanbase, it gets intensified. One watch at it (or just lurking in the episode threads), and voila, profit, the ultimate review that illuminates the rest. 

> Do I give it the rating of how I felt or do I knock it down a few points because I don't think it would be fair to give it such a rating. Personal enjoyment vs quality.
the big eternal debate that definitely will accompany us when it comes to any review. Rating it lowly or highly because I like it or not despite its quality or giving it a technical score despite its enjoyment?
Many have rated Yakity-Sax  or the recent episode because it didn´t fit their expectations or taste. Many experts recommend to give something more than a watch in order to have a mindset and notice the details behind it and leave the personal mindset aside. 

If we have such trouble with a kids show, then we are fucked for justifying and explaining precisely existential things such as the origins of the universe or any future event.