Ok, so now I have an impression that MnF is an original story built around "what happened to the missing SM crew".

EF seems to perfectly fine until the battleship came in.
Thats how the story starts as it appears to me in the comic.
23 years ago.

Maybe theres still an unrevealed original bad guy pulling the strings, making use Einst and SM andriods?
Got a feeling that there has to be the one bad guy, the last boss.
The pirates and cat guy don't seem so bad to me.
The Orchestra Army look pretty like one tier up to the above mentioned to me.

23 years.
Could those "Akuma" that came from Formula Heim be Einst?
Or an original bad guy army/race?
There are no characters for Formula Heim yet also.

Another point is what are KOS-MOS and the NxC originals purpose in the game.
Just plainly to add to your party?
Could the main bad guy be a crossover?

How much could the info revealed currently is?
The first quarter of the game? Half?