Storyline questions, so spoilers...
1. How was High Charity able to reach earth when it was clearly stated in Halo 2 that most of the power for the city came from the engine of the forerunner ship? Surely the reactors could have powered some systems, but it must take a decent chunk of power to move something the size of a moon through slipspace.
2. How did something that is mearly a giant slipspace drive shield humanity from the first halo firing? If some humans had been taken to the ark, how did they get back to earth with no forerunners around to fly them back? Did all of earth perhaps get transported to the ark and then sent back when the firing was complete?
3. Did they original Halos get fired by the ark remote or was an index merged with one halo leading to all of them firing? If activated from the ark, what happened to those who activated it? They would have been well outside the blast range.
4. Why did Gravemind not infect the earth before going into the portal? Surely he could have used a few billion more warriors...
5. How did Cortana know that there would be a new Halo being constructed on the ark, thus offering another solution to the flood without firing the other rings, when the Gravemind and even Guilty Spark were totally unaware of this? She couldn't have gotten that info from the first halo because then Guilty Spark would also know, and she couldn't have gotten it from her encounters with Covenant computers because then the Gravemind would know. Both Gravemind and Guilty Spark were surprised when they found out about the new Halo, so neither of those explanations make sense.
6. Last but not least, did Truth really believe the stuff that came out of his mouth? All of the stuff in said in Halo 2 would indicate yes, but then he said in Halo 3 that the Forerunners had to set aside their compassion and do what needed to be done. Why would you need to set aside your compassion to send yourself to heaven/become a god? If he really thought that they had made themselves gods, why would he make such a comment?