Iron Man ... perfect characters for action games
He has an incredibly versitile arsenal of awesome destructive power, yet he's not so powerful that you'd need some crazy shit kill him (even something as "grounded" as a tank is a good threat)
He can also fight at both long and close ranges, he can fly, he has the brains and pockets to build cool tech and he has a very diverse range of villains and threats you can set the game in pretty much any type sci-fi scenario
In regards to game structure
Imo the best way would be to make it mission based
That way the devs could make each level its own unique experience - busting out of his captors cave with the Mark 1; dogfight over the Atlantic against an AIM flying super carrier; infiltrating an underwater Hydra base with Namor as constant torn; battling the Crimson Dynamo over the peaks and valeys of the Alps; finding and capturing the Hulk on the Grand Canyon; surviving an assault by Living Laser, Ghost and Blizzard on Stark Tower with one of the more simple suits; big mech fight against Ultimo; dungeon crawl through Doomstadt; liberating a small island nation (with the caveat you can't harm civilians); showdown agaisnt the Mandarian in a dimension of his own creation.
Gameplay would be largely dependent on the suit used
Mark 1 could largely play like infantry power armor - heavy, clumsy, can't sprint, no repulsers, can tank anything bellow .50 cal, can carry very big machine guns, has flamethrower and 2 missiles equiped, bestows superhuman strength - but perhaps with some serious vulnerability because it was built in a hurry with scarps (say the back isn't plated, like we see in the 1st movie)
Mark 2 would be the simplest version of every armor going foward - weakest protection but no vulnerable spots, no oxygen tank so Tony can't fly very high or go underwater, only weapons would be the repulsors and unibeam, can sprint and perform complex melee moves and since it's the lightest armor it has the fastest takeoff, flight speed and draws the least power from the arc reactor
Aside from these 2 suits, all other armos would be player created with a multitude of custom parts, weapons and stats to keep track of their performance - of course there could be a few other pre-made suits for specific missions, like the hulkbuster unit, the giant mech for the fight against ultimo, perhaps even a secret overpowered suit that can only unlocked by completing a hard challenge
Finally keep cooldowns to a minimium - intead use ammo for "convencial" weapons and energy drawn from the arc reactor for every other suit ability/weapon (unibeam being specially costly), with dire consequences for losing all power to the arc reactor
how to best implement flying superheroes.
Nothing to it
Despite the shitshow, Bioware's Anthem actually did that quite well
So did Just Cause 3 and 4, with its jet wingsuit
Fuck GTA4's Iron Man mod did it relatively right, even with the jank I still had a blast with it when I was 13