dude halo was influenced from marathon but is the prequel to the marathon game, its not stated that the main character from marathon is the MC nor will it ever be until a game is made. but it is after halo they are in the exact same time line its even stated in the wiki of both games. The USEC could be a result of the old alliances of Earth reforming due to the fact that the war with the Covenant, which brought earth together has been defeated. Same as in if you ever read Enders game, the forces untied for the greater good to destroy the alien threat, mission achieved the old alliances are back. USA, Russia, UK, Japan, China all of it save part of Africa because its been glassed. As for the AI think of the original Marathon as a beta of what is to come, same as halo 1, 2, and 3 beta it wasn't final it was the thought at the time. But so many things are the exact same from Marathon to Halo, you can argue that well they based Halo off of it which i know they did, but i still believe it was to tie everything back to Marathon. Cortana should be dead but who know if bungie was going by the books alot of things would be different, i know that some books were made after halo 1 was released but you would have thought they would have based halo 2 off Halo:First Strike. So all in all we arn't for sure until bungie tells us whats going on, seeing as how lots of Halo 3 speculation was dead on im sure alot of speculation about the Halo to Marathon will be also.
Funny how H3 hasn't been out long and were talking about what will happen in the next game. If they would have simply killed the MC then it would have been done. But then they would have lost fans and money lol.
Edit: the main character came to the USEC ship Marathon he didn't fly it there.
another edit: here's an image from deviant art that a fan of marathon made of the main character look kinda familiar?
another edit lol: wiki page for Marathon-
http://en.wikipedia.org/wiki/Marathon_Trilogy
notice how it mentions that halo and marathon are similar, it doesn't say much but gives a little insight on how it might be related.