Charming... though, not really much else.
Look, "MMMystery on the Friendship Express" is certainly a good episode. Not a great episode, but a good episode. It's exceedingly silly, and takes itself even less seriously than most episodes. However, with a weak narrative and a poorly supported moral, the episode fails to be much more than entertaining filler.
The thing that "MMMystery" has gotten the most flack for is its simplistic mystery, which is almost immediately undermined by barely even trying to hide the actual perpetrators. Indeed, in the scene where Pinkie's guarding the cake, Rainbow's outline can clearly be seen, and Fluttershy's not hidden very well, while evidence for Rarity taking a bite is placed right out in the open. This makes the story hard to be invested in, but it seems that watching the characters' reactions is much more important than the mystery itself.
Indeed, that's where the episode's humour comes from. Pinkie and Twilight are bounced off of each other to pretty good effect, resulting in an abundance of silliness. The homages in Pinkie's wild accusations are also quite fun, though they too are lightweight and silly. The episode is definitely fun, having a breezy pace and consistently silly dialogue. Not much is done with the animation, which is mostly just in service of the silly script.
Unfortunately, there's almost nothing in the way of character development in the episode. For some odd reason, it does have a moral, but it's not supported very well by the episode itself. Sure, Pinkie makes wild accusations, but they're not shown having much in the way of consequences, and there's certainly not much of a reason to actually learn anything. The moral is at least something worth learning, and its core about not making ignorant judgments is something the periphery demographic can appreciate, but it's not built up to very well in the episode, and there isn't much of an impression that Pinkie has actually grown as a character.
It's all fluff, really. The jokes are lightweight, the story isn't very good, there isn't a lot of character development, and the moral isn't built up to well, but it is at least entertaining. It's filler before the big finale, and as a little something to keep fans busy until then it's pretty effective. "MMMystery" certainly isn't a bad episode, but I can't imagine many people calling it a favourite.