Man of Honour
Very little in the endings, other than a degree of standing you have developed with Johnny, connects with what you've done in the rest of the game. One of the things which lets it down significantly given the genre.
They've obviously had a bunch of parts designed for another vision of the game and had to glue them together as best possible to get a, not the, game out the door.
I agree that's the reason why the game is so often disconnected in terms of the results of choices. Where your choices have any effect, it's usually limited to 1 person or 1 location. I also think it's the reason why there are relatively few choices in the game.
Either that or the whole game design process was so incompetently done that different people were working wholly independently on different parts of stories without any overall plan, so it was always going to be a matter of disconnected parts. But I think that's less likely.
Which is why I don't think we'll ever see the game it was hyped to be as they'll basically have to take it apart again and make another game. IMO it'll just be bug fixes and a bit of extra DLC while things like the lacking crafting mechanics, etc. remain largely as is.
I think they might also fix some balance issues and they might also make the UI less rubbish, but nothing more. I think they might have a go at making the game they claimed to have made (and apparently intended to make) next time, in the sequel. As you say, to make the game it was hyped to be they'd have to essentially make another game. So it would probably be a better approach to make another game rather than spend the time remaking this one.