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: Phineas And Ferb Mission Marvel
Broken Base: The initial announcement that such a crossover would happen, though the episode has mostly been well-received now that it has been released (at least among more casual viewers).
Phineas's anger at Candace through much of the episode is the main point of contention, with many considering it too abrupt and too out of character.
Hilarious in Hindsight: Prior to the episode's release, many were apprehensive about how the Marvel characters would be characterized. After the special aired, it turned out that it was the characterization of Phineas that was most divisive.
Unconventional Learning Experience: Though Candace pointing out that energy can never be destroyed is based on her reading of comic books, the rule also applies to real world physics, which children watching this show may not necessarily be familiar with.
Unfortunate Implications: The other supervillains having no qualms about working with Red Skull, considering the whole Nazi thing. He's never called one in-universe, true, but that doesn't mean he isn't one.
The Woobie: As always, Candace, who can't help but screw things up every time she tries to help (until the end of the episode), to the point where the normally cheerful Phineas yells at her several times and revokes her S.H.E.D. membership. She even sings a sad song about her predicament alongside Isabella.
They Wasted a Perfectly Good Plot: Many people feel that Isabella's issues that made her feel useless should've been elaborated on more outside of her song with Candace.