TwilyEllie

And I know that sheep and cows in the show do occasionally speak, I just mean this in the sense of actually living in their own villages in different parts of Equestria, rather than being mostly depicted as livestock that only speaks as a throwaway gag.

Oh, I would change a lot. But also a lot of things would stay the same. The broad strokes – the core structure of the story – would probably stay mostly the same. Starting with the first episode, Nightmare Moon would be explicitly recognized by the ponies from legends – they'd simply be in disbelief that she was actually real, standing before them in the flesh. It really seemed off to me that absolutely no one knew who she was, even though the legend would surely be known by others, as was established in the later episodes. Second, more creatures. Sheep, cows, etc. should've gotten some more love, depicted as fully sapient, independent beings and drawn in the same cute style as ponies. (Art by TwistedHiccy) And I have to say, I'd probably have been quite a bit harsher on Discord. It annoys me how everyone just puts up with him even though he keeps deliberately causing trouble for everyone.

A crossover episode featuring all of the Mane 6 would actually be unlikely to answer what happened in the time between the two gens. Note that the Mane 6 would most likely appear as their past selves – possibly after Twilight's coronation, but long before The Last Problem. Meaning that to them, whatever happened between G4 and G5, simply didn't happen yet.

If any of the Mane 6 return, it might just be Twilight, as an ancient alicorn princess standing taller than Alphabittle. Alternatively, time travel shenanigans can give us a crossover episode with all of the Mane 6.

Larger than she is in the main show, but not Celestia-sized like Twilight. I would say most likely to be Luna-sized.