Both Equestria Games and Filli Vanilli I consider good episodes myself of course.
Though Filli Vanilli is I suppose weird when you take into account all the songs that the Main 6 have done in the past. I guess for some reason that the majority of the songs that weren’t being performed are just a scene of the episode being done like how a Musical does things regarding the plot?
I believe there’s a theory that came out after the episode that In reality the Ponies would not be singing at that moment, but to show how the characters are feeling in a more fancier approach they have them sing in what’s shown to us? Think about why Disney includes songs in many of their movies. Are they there because the character likes to sing? That can be a reason why, but I don’t think that’s always the case and I think it’s more common to see DIsney include songs for the reason of “It’s Disney” and not because of the characters. They include songs to provide a much more entertaining way of showing what the character singing’s motivations or even dreams are sometimes. We see Frollo, the main antagonist from The Hunchback from Notre Dame sing “Hellfire” to express his inner conflict he has about falling for what he calls a Gypsy. It’s probably far more entertaining to the audience for him to sing about it in a Villain song then it is for him to just be talking to himself about it on screen. Which might be technically what he’s doing at the moment, but we don’t know that because we’re offered a pretty cool music sequence to go around him instead of just him alone talking to himself with nothing else to add visually or otherwise no enhancements done to drive the point of what Frollo is trying to say in a way that isn’t that entertaining to watch.
The same goes for a majority of the songs in Friendship is Magic. Magical Mystery Cure could basically be all this as obviously the events of MMC are not done in 22 minutes as the episode begins in the morning, and later comes up during the night, and then finally days or even weeks later when it shows Twilight’s coronation. The musical approach was pretty much the only way they could really show off all the complex feelings of the story and make it so that alot of the story could fit under the 22 minute timeframe. Meaning it’s quite possible that for the exception of Pinkie’s random songs that were quite prominent in Season 1 and any songs that are implied to be a performance, that most of the songs of the show did not happen in Reality as they’re more there to show us a far more entertaining way of exposition, showing how a character is feeling, or other kinds of usage for songs.
TL;DR version: The Filli Vanilli and previous Music situation can be explainable if you go into the thought that most songs that were not some kind of performance (Examples: “You Gotta Share, You Gotta Care”, both Flim Flam brother songs, etc.) actually did not happen in reality. When’s it’s just a much more dramatic and/or entertaining way of expressing what’s going on with the character(/s) who is/are singing at that time.
Also as a side note, regarding Fluttershy and the CMC you must be referencing “Hush Now, Quiet Now” which I don’t think would be like singing in front of a crowd because I imagine Lullabies are easier for Fluttershy to do especially for Animals or in this case children.