These are what we call the 'YMMV items.' Things that some people find in this work. We call them 'your mileage might vary' because not everyone sees these things in the same way. This starts discussions in the trope lists, a thing we don't want. Please use the discussion page if you'd like to discuss any of these items.
YMMV: The Magic Flute
Alternative Character Interpretation: There are some who believe that the Queen of the Night was the good guy after all and Sarastro really is the Big Bad. Particularly common with feminist re-interpretations of the opera. After all, throughout the first act it's really only the Queen's word against the Priests' and Sarastro's on who's the good or bad guys. Their main argument why the Queen's side of the story is false is because she is a woman. It isn't until the second act that she really goes crazy.
Everyone Is Jesus in Purgatory: Some people will insist that every single thing in the opera is a Masonic symbol, including that the music being based on triads symbolizes the Masonic significance of the number 3.*
For those who aren't familiar with music theory, music being based on triads is People Sit On Chairs for Western Classical music.
Family Unfriendly Aesop: The "very good reason" Sarastro gives for abducting Pamina is that she needs to learn to let men guide her. That doesn't play so well nowadays, obviously.
Again, this was dictated largely by the political views espoused by Schikaneder, favoring the "Enlightenment" values esposed by Joseph II against the old-fashioned values of Maria Theresa. (Of course, one of those new Enlightenment values was the idea that women were naturally irrational and unfit to rule.)
Older Than They Think: The Queen of the Night is a part for a soprano diva, with very challenging music and some of the highest notes a soprano is expected to sing, in the midst of an opera that includes mostly simple music written for performers who were actors first and singers second. Mozart may be the best known composer of this type of role, but it's actually a tradition going back to earlier Singspiels rather than a new innovation in the format.
The Scrappy: Monostatos; in most productions he isn't the least bit funny.
Which would make him an Ethnic Scrappy if you're dealing with a production that is faithful to the text, as opposed to ones that omit the racist elements of his character.
They Wasted a Perfectly Good Plot: The Queen of the Night's plot to have Pamina assassinate Sarastro is resolved in a single scene. At least the princess gets another reason to languish soon enough.
Sarastro and his priests have some pretty misogynistic lines at times, which are generally Bowdlerized during the translation from German. Not to mention that it's the female ruler, and her black Dragon, who get cast as the baddies...
They're actually not always Bowdlerized. Unlike the racism in the scenes with Monostatos, the anti-woman lines are found in the music as well as in the spoken text, so they are harder to just eliminate.
This was mostly done to fit the Freemasons' beliefs about how men were superior to women (not that the Freemasons were unique in this belief in the late 18th century).
It can also be argued that while Sarastro is presented as the "better" choice between the two camps, his position is too extreme. Note how Pamina, acting on the information of the boys (the only group that is not really on either side), apparently breaks the priesthood's rules and reminds Tamino to use the damn Macguffin, probably saving everybody. Very likely a much stronger feminist message than Mozart and Schikaneder intended, but ridiculously easy to incorporate for a modern audience.
In fact, this is discussed in the work. Well, kind of:
Ein Weib, das Nacht und Tod nicht scheut / ist würdig und wird eingeweiht.
(A woman who does not fear night nor death / is worthy and will be ordained.)
Monostatos in general. He was originally intended to be played in blackface, and Pamina is scared of him largely because he's Black. The racial element is usually glossed-over in modern productions, if not omitted entirely (by simply using race-blind casting - which is pretty standard in opera these days - and omitting all references to his race).