System Shock 2 gameplay.
Set in floating Ultra-America.
Themes of morality (alternate selves & choices), nation states at crossroads (America has many great examples to use), and the significance (or lack of it) of father figures as both literal and metaphorical entities. Could also cram in some crap about religion or whatever, but I think the game as it is veered away from that because it didn't mesh well. I don't know why Comstock was a prophet and everyone was religious; it worked for the metaphor and the ending, but having Columbia be a theocracy undercut the American aspects; they should have been strict Constitutionalists who are also religious, not submit to religious rule.
Go back to buying charges of Vigors. Have your purchases at shops affect the world in some way, by fueling the economy. Stuff can have different prices in different dimensions. Could explore the moral consequences of that.
Open world. Some areas locked off at the start. Also able to move between realities with a little more freedom, but perhaps some major limitations. Instead of it just being a story mechanic, it could be used to willfully go back and forth, but only at great expense or effort each time. You may not always be able to go back, etc etc.
Fix the gunplay. Make guns less accurate buy more deadly. The gun handling was awful, but the game made you move a lot, scrounge for ammo or a new weapon mid-fight, and actively discouraged camping behind a single barrier. That was the best part of the gameplay: running & gunning and being rewarded for it.
More Mecha-Founders; those were awesome.
The E3 gameplay has good examples of what else needs to be done.
Songbird chases you everywhere. No matter what dimensions or where you go, it's searching for you. You have to hide, or try to fight him off, which should be almost-impossible, especially for a first-time player. Maybe have segments where Elizabeth can be captured and you have to go fetch her before you can continue the story?
Dynamic fights. People sounding alarms (if you don't kill them) to summon Zeppelins, able to spawn in actually-useful items
Dynamic social interactions. Different factions can treat you differently. Crazy people prone to attacking. Ability to offend entire groups of people and start a literal riot.
Big platforms that are connected by a realistic skyrail network.
Maybe more horror sections, or bits without Elizabeth, or possibly both combined… you get some alone time and the tone and gameplay change completely. Emphasize her usefulness by limiting you, but also challenging you in different ways. Could break up monotony, if any builds.
Setting was great. Writing was overall pretty good for a video game. It's too bad the gameplay was so terrible. E3 demos looks great; I'd have happily played that game.
Game is totally fixable… if you keep the aesthetic, and the general story, and build out the gameplay from scratch.