Every character in this game is either a stereotype or just generally weak. I didn't even know who Armstrong was until the final boss, but maybe that is due to my bad attention span.
Either way I think it would have been awesome to have Solidus Snake/George Sears reappear somehow. I guess it would have been possible to retcon through cyborg brain technology or whatever, involve the patriots in some way I don't know; it wouldn't have been the worst retcon this series have seen thats for damn sure (god damn MGS4 was a horrible game, it's excluded from my personal canon lol but that's for another rant). Of course he would need a lot of screentime and I guess this game isn't really about rich story as opposed to good gameplay.
I think the history between Raiden and Solidus is really interesting, and having him as the final boss would have made the game very memorable to me. But I guess it would be a bad thing to trivialise the amazing conclusion of MGS2. At the end of the day I guess it couldn't work out well, but the story in this game just feels pointless to me.