Marvel actually had a fantastic tone in the entire Cap/Thor/Iron Man/Avengers saga. Regardless of the writers’ politics, the theme of a Bill Gates-like Thanos wanting to kill half the universe for “balance” was unmistakable. Likewise, many of the lines (esp. in “Avengers 1”) were memorable.
Black Widow: “Cap, you can’t go after them Those guys are gods.”
Cap: “There’s only one God, ma’am, and I’m pretty sure He doesn’t dress like that.”
Also, in the movie Civil War there is an argument about where power should lie. Stark wants the Government to be in charge of the Avengers; Cap believes that the power is best left in their own hands. Toward the end of the movie, you see that Stark's govt. approach has all of the Avengers sitting in jail cells. Stark seems surprised by this; but, we know that this is where the govt. control will lead. Cap was right.
The other thing that people who dismiss these films as simply "comic book movies" are missing a lot of very entertaining films. Another amazing thing about these films is that the Producers put together a string of 18-20 (don't remember the exact number) movies that fit together, one following the other and all culminating in the final two movies that tie everything together.