I think Captain Marvel is definitely the right name to call her as far as the story goes. Nothing else makes any sense - except 'Warbird' being her callsign, but that's an antiquated codename or a reason. It's just that when you say "Marvel presents: Captain Marvel" you give the impression to some that this will be the ultimate Marvel movie, and to others that this is the cheesiest Marvel movie. "Captain BlahBlah" is kind of code for cheese. Cap gets away with it because people kinda know he's Cap, and expect him to be cheesy but in a good way.
I think you can remedy it best by making "Captain Marvel" the ultimate Marvel movie, in terms of what people like about Marvel heroes, where Carol is very much a normal woman with normal problems that gets caught up in this epic superhero thing. She becomes a proxy for the audience not just into that film, but into the world of superheroics in general as she sees Mar-Vell and his larger than life adventures. Because she is not-powered for most of the film, she becomes a type of fan, in the literal sense, of Marvel. And then she gets the ultimate wish fulfillment... she gets to be the superhero.
As for the marketing, market it as his movie. I know some people don't like the switcheroo, but it's kind of what makes Carol, and indeed, the whole idea of a legacy hero, work. He's the one who is a mild mannered scientist, with a dark secret he's trying to hide from those closest to him. Problems? He's got all the problems you could ever hope for, from late rent to issues with his girl/crush/coworker Carol to terminal illness... and he's got power that drops jaws and aircraft carriers alike, and he's facing nothing less than a full on alien armada... all by himself... with may be Carol cheering him on and flying a little jet or something... Show all his best work in the trailer, and let Carol be the one who is a complete surprise, in the way that she does everything when it comes to release day...
Oh and show the name at the very end of the trailer, with a very frayed, distraught texture to it. Like the word Marvel is cracked/fractured or something. That should pretty much dispel the "Oh Marvel's got a superhero named 'Captain Marvel,' how predictable." stuff.
Longwinded, but that's how I'd do it... of course, his death would be as predictable as Gwen Stacy's then, wouldn't it? But then again, you could hire an actor on for just one film and get someone really really big like Pitt or someone on the caliber of the villain actors they've gotten. It wouldn't hurt to have three films in the contract though for Mar-Vell, one for a flashback, one for a timewarp scenario.
Edit:
Random Dialogue of dubious quality
Danvers: "Okay, let's start over then... I'm Major Carol Danvers, United States Air Force. Your turn."
Lawson: "If you wish. Pluskommander Gheneris Halason Mah'r Veh'l, Kree Imperial Navy"
Danvers: "Pluskommander? That's like..."
Lawson: "Captain, more or less..."
Danvers: "So... Captain Ma... Muh...."
Lawson [with truly alien accent]: "Pluskommander. Mah'r. Veh'l."
Danvers: "Okay, Pluskommander... Mar-Vell?... wait... you're not seriously telling me your name is Captain Marvel!? Seriously!? [quietly, to self] I want a cool name like Captain Marvel