IF cortana has to go there's only one way to make up for it: The MC finds one or some of the few remaining spartan-IIs that are still alive out there somewhere. I doubt cortana is gone for good though as there are several sound theories (for the halo universe) to how she could still exist. I'm hoping by halo 6 the MC has both cortana and some other spartans-IIs on his side. After reading all the books (besides the forerunner series and the two books that take place after halo 3/4), I don't see how they could ignore these last few spartan-IIs.
RANT: I would also like to point out that i didnt like the halo reach game. Why? Because there were hundreds of spartan-IIs, like the MC himself, putting up a losing fight on reach too. Instead, bungie decided to tell the story of the spartan-IIIs that don't even compare. The reach book was even rereleased with some extra pages for the spartan-IIIs AFTER the game came out. Simply, a much better story could have been told in the Halo Reach campaign. /rant