I noted before that the "20 Things Wrong With [Amazingly Successful Franchise Film]" articles are sad, then wrote just such an article. This is a very short one for a very few of the things about MCU movies that are most bothersome. To me.
Complete inconsistency in relative strength: the battles are what's actually important here, and even so, there's no rhyme or reason. Yes that keeps the audience interested and serve to advance the plot but come on, most powerful guy in the universe hits a mortal with no special armor or anything and they just get the wind knocked out of them - but he can knock down Thor or the Hulk? And he constantly doesn't take obvious shots?
Zero sum thinking: I get that Thanos is a bad guy, so his message - that there are only so many resources, and more and more mouths to feed - is not the one the good guys agree with. Yet the franchise appears to endorse it. The disappearance of half the life on Earth would be first, economically catastrophic. Guess what? Smartphones and corn don't just grow themselves out of the ground. Plus, the specialized knowledge required means that the disruption in productivity would actually be more than a 50% drop. Imagine your company's level of functioning if 50% of people called in sick tomorrow - it would be much less than 50%. And of course, the disappearance of the Earth's oxygen-producing organisms, plankton, etc. would be much worse.
Profound scientific incuriosity, including by career scientists: "Hey, I'm on Asgard! Should I maybe try to pocket a few pens or take a few pictures, ask people how things work? Nah, I'll just hang out and get all wrapped up in my personal issues." Incontrovertible proof of aliens on Earth by their repeated attacks, but no mention of a second Copernican revolution in decentralizing mankind's image of itself, or trying to get the alien tech for more than for the Avengers to make better guns. No attempts to start trading or at least communicating with aliens. Also, Thanos's snap would answer a bunch of questions - for example, which things are alive or not (did half of prions disappear? Viroids? Kind of weird that no wombats disintegrated, I was always suspicious of those things. However, Galaxy S5 phones disintegrated but not S4's, so that must be the sentience boundary.)
If these things start to bother you, though you can never really return to your previous innocence once you've noticed them, you can over-intellectualize and get partway back. Rather than criticize these gross inconsistencies, you can think of these movies as modern action-expressionism. The original expressionist film movement is often described as portraying the (actually more important to the viewer) inner emotional reality of the narrative, rather than the superficial matter of the characters' physical world. This coincides with the hyper-reality discussed by Umberto Eco (i.e., where for example artificial lemonade is more lemonadish than any real lemonade ever was; the California Adventure section at Disneyland is more like the Sierras because it purifies and concentrates all the salient aspects of the Sierras, etc.) Alternatively, you could think of the MCU movies as magical realism, where the magic is focused on violence rather than relationships. Or, that MCU is modern-world fantasy in the same way that Star Wars is fantasy; though it takes place in space, exploration of the science is absent, and there are wizards and sword-fighting.
Finally: THERE WILL BE A STAR WARS-MCU CROSSOVER BY 31 DECEMBER 2028. Anyone willing to bet? And the way things are going, it will be Disney trying to use MCU to salvage Star Wars rather than the other way around.