My #1 favorite MCU movie has definitely changed a bit over the years. It started with Iron Man, then the first Avengers movie, then Civil War, etc ...
As time has gone by, though, I'm going to have to say that I think the first Iron Man is Marvel's best. Amazing origin story, fantastic performances, awesome showcases of "powers," etc. I've always flat-out adored the film, but for me, it has aged like a fine wine, and I think it sits above the rest in the MCU.
I just find the first Iron Man movie to be the most effortless, if that makes sense. It was a "lightning in a bottle" situation, if you ask me.
The structure and pacing of the film are top-notch for me as well. To this date, very few comic book movies since have matched the "edge of my seat" escape sequence from the first Iron Man. And very few lead characters in comic book movies have been nearly as charming as RDJ's Tony Stark was in that first movie.
If there was anything I could really change or improve upon the first Iron Man movie, I would have cast Don Cheadle from the get-go (even though Terrance Howard's performance was more than okay).