Since the Marvel Cinematic Universe has been around longer than the DC Extended Universe there are many more references to things from the comics. For example in Captain America: The First Avenger you can see the tree of life which is a reference to the Asgardians from Thor. In a scene from Guardians of the Galaxy when they visit the collector you can see the celestials who are an important group in the Marvel comics.
I would like to see the Secret Invasion story appear in a MCU movie. This is a story in the comics when the the Skrulls secretly replace different Marvel heroes with Skrulls, since they have the ability to shapeshift. This would be similar to this last season of Agents of Shield where the characters were replaced with robots, except on a larger scale and with more well known characters.
I would also like to see the second civil war from the comics appear in the MCU, but this may be difficult because it involves so many mutants that Fox has the rights to.
I also think it would be interesting to see the MCU crossover with the DCEU, like when Marvel and DC crossed over in the comics. However this is very unlikely to ever happen.