Yes, I took the Atlas. Frankly I can't imagine trying to survive that last bit without it. I'll say one thing about ME3 - the combat is a lot more difficult than ME2. More swarming from all sides.
I did take EDI on the Grissom mission. I rather enjoyed that apology.
There are novels? I may have to check them out since I really like the universe.
Yeah, there's four novels and a bunch of comics. None of the books are what you'd call literary masterpieces, but the first three novels are written by Drew Karpyshyn who IIRC was the lead writer on ME 1 & 2, so the tone is pretty consistent and the lore is all correct.
The first one tell the story of a younger Anderson trying out for the Spectres with pre-indoctrination Saren; an incident briefly mentioned in ME1. Along the way he meets Kahlee Sanders who becomes the central character in all four books and you get hints as to how Saren would eventually discover Sovereign.
The second book takes place just after the original Normandy is shot down IIRC and mostly concerns Kahlee who's now working as a teacher at Grissom Academy, one of her biotic students--an young autistic girl named Gillian--her deadbeat red sand junkie father, his connection with Cerberus and some shenanigans that ultimately involves the quarrian migrant fleet. This incident is actually mentioned in ME2. Remember how the quarrians reacted to Shepard being with Cerberus? This is why.
The third one is basically a follow up that links into what the Illusive Man is up to ME3. It takes place after Shepard's suicide mission, but before 'Arrival.' Kahlee is back at Grissom Academy and even reunites with Anderson. You may have already heard the name Grayson mentioned here and there in ME3. That's a reference to the events this book.
Don't even bother with the fourth one. Seriously. By all accounts it's complete and total garbage. A real incompetent hack job, even by the low low standards of a video game tie-in novel.
P.S. In case you didn't guess already, the character from the novels that appeared at Grissom Academy was
Kahlee Sanders.
P.P.S. The comics are of variable quality and relevance. They mostly "fill in the blanks" type stories meant to bridge the gaps between the three games. The first major one tells of how Liara got Shepard's body away from the Shadow Broker and how Feron ended up captured. The second tells the backstory of TIM in an incident that took place right at the end of the First Contact war. The Third is about how Cerberus took Omega away from Aria and there's one ongoing series now that tells some of the backstory of each of the main characters from ME3. Not sure if it'll just be squadmates, but so far they've done Vega and Tali. There's a few others, but they're just little snippets. Mostly single page web comics.
I did find this:
But what an end! 
