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[VoodooDrackus]

My first playthrough ended with just 2 choices. Control or Destroy. My EMS rating was below 2000.

I decided to play through the ending part again before going to Earth after getting my Galactic Readiness up to 100% via Multiplayer. My EMS ended up at 5200.
 
I did notice that the fleet was so very massive compared to the meager one I had during my first playthrough, but I still only ended up with the same 2 choices.

It turns out you have to go back to the part before you go after the Cerebus base in order to have the EMS rating effect the ending. This also gets you the Master and Commander achievement/trophy if you are into that type of thing.
I blew through it on the Narrative difficulty. Took about an hour from the Cerebus base to the end.