Thor has to be my number 1 choice. The character is pretty unrelatable, he's a big blond god - but the characterisation that they've used, where Thor isn't taken too seriously (and doesn't take himself that seriously) has been really enjoyable. A lot of people moaned about Thor TDW, and while it had some weak points (villains being one of them, Kat Dennings another) I found overall the movie tremendous fun, and the Thor-Loki relationship gets more entertaining every time they meet up. All in all, I think making Thor an engaging character is probably the biggest ask, of all the main Marvel heroes. As such, I enjoy him the most.
As for the other main characters, Tony and Cap deserve a mention.
I've always loathed Cap, but his last two movies were so good that I'm starting to change my opinion of him - the Russos do brilliantly with the character, and Evans has really grown into the role.
I initially loved RDJ's Iron Man, but found he stagnated as a character throughout Iron Man 2, 3, Avengers and Age of Ultron - which are all just more of the same stuff. But, in Civil War the character took on a lot more depth and introspection.
Mind you, Civil war is just a superb superhero movie - really I think of it as an Avengers film rather than a Captain America film, because so much of the action and story relies on the other characters. Hell, it sucked me in, and I'm a hard core DC fan - and really none of the Marvel characters in it are those I really cared about (as a kid I was partial to the X-Men, but never cared for the Avengers). Anyway, Civil War was so well done that I actually gave a **** about how it turned out. And the action...superb ! Cap/Bucky vs Tony was everything Batman v Superman should have been (I hope Snyder took some notes !)
I mean, in B v S, the whole mother thing was just terrible, but in CW, when Tony sees the video of his parents' murder....man, I got a bit emotional. That fight has so much emotion invested in it - and the way it develops is completely believable (in terms of superhero fights) it's back and forth and of course Tony has the upper hand - but hesitates from administering the coup de gras, and of course Cap ultimately wins and at the same time loses.
Yeah, it's simply great, probably the best fight scene in a superhero film - or at least the most emotional.
Maybe that says more about CW as a movie, that it could make me really care about characters I ordinarily don't give a toss about. A total triumph in the cbm genre, which it has lifted to new heights.
But I digress, Thor gets my vote, with Cap and Tony a close second.
t: I think RDJ is a massively underrated actor.
Fair enough. 
