How would I do it? Hmm... that's a difficult question. Honestly, like others have already said, I would keep it largely the same. I think Kevin Feige has done a great job as the architect of the MCU. I would probably keep the movie slate the same, since Marvel did such a great job overall with the Infinity Saga, I feel. Not being any sort of film creative, I wouldn't have the confidence to change the overarching story to something else and feel it'd succeed.
That said, I would make efforts to create better versions of the films: The Incredible Hulk, Thor: The Dark World, and maybe Iron-Man 2 and 3. I do have an amateur interest in how movies are made- everything from writing, to cinematography, to effects (I watch any special features I can)- and one of the things I've learned is how difficult it is to make a good movie, given how many moving parts there are. And then there's the dreaded studio interference we all know about. So ultimately, I don't know what concrete efforts I would make to cause these changes.
Visually, I would make some changes. I would definitely improve the color grading from the start. Add in some true black to the scenes. And something I've thought about from the beginning is making each movie more... distinct. Don't get me wrong- I love that they're in the same universe and we as an audience can tell, but they all just seem to have the same "look" to me- maybe like they're all working in the same color palette or something? I don't know. It just seems like the non-MCU movies are more visually distinct: compare the first Spider-Man and X-Men. A part of me just wishes that the movies had different "artists", like the comics do. I'm having a hard time articulating this point, so I'll cut it off here.
Lastly, I would do something about the film and television divide. Maybe I would've brought the characters over to the movies. Maybe I would've even rather have no shows at all. I just know I don't like how it all went down. Like Bob Iger said, "There shouldn't be two Marvels."
Well, that's all I can think of- for now at least.