Also, in case you don't know the Marathon storyline, they find the cyborg with an AI named Leela. This could very well be Cortana. As for the name differences, Cortana has shown signs of rampancy in Halo CE, 2, and 3. An AI becomes rampant whan it finds out that it's not real. While being alone (MC is asleep in a cyrotube so I dougt that she'd wake him up for a conversation), over 200 years, she could become rampant and forget who she is. When the soldiers on Marathon find MC and Cortana, they can't find out Cortana's name, so they nickname her Leela. Also, over 200 years, there is a chance that some of the species will evolve in to the Pfore. I think that Hunters will evolve into the Hulks somehow, and the Sentinels will turn into the *hard to spell name here* and the Sentinels might even be taken over by remaining flood, making the robots in Marathon look less robotic like. Also, I have a feeling that the grunts evolve into the Pfore troops. If you look at some of the drawings, the heads of the grunts and the Pfore troops look the same, except for the fact that the Pfore troops have three eyes. If you look on Pforepedia, and you look up the Pfore race, the discription of them states similar characteristics as the grunts. Both extraterestials have: grey skin, red eyes, live in a caste system, and both use a breathing apperatus (although the I don't know what the Pfore breath). Anyway that's just what I've found.
[Edited on 03.15.2008 7:33 PM PDT]