Some talks are already out concerning the different alliances and their weirdness, especially Orks and Imperial Guards.

the WH40K universe being so vaste and filled with lore, it would be awesome to include in the rulebook or a separate mini novel in the core set a story background explaining the different struggles and goals of each factions and why some are allied with others.

That would give us an awesome background story of the game and would explain a lot about the alliance choices of every factions.

What do you guys think?

Considering the load of codexes and novels that already exist it's unlikely FFG will make one. But maybe Black Library will print a Conquest novel since they do all the GW fiction.

They might also do small story type inserts in each of the packs like they do with Android Netrunner.

it wouldn't surprise me. ANR packs have memos form major characters and email dumps form the hackers in them and a set story. CoC has actual short stories in normal narrative just like a book that you read like a magazine serial, a page or so a pack.

I think this would be a great idea for 40K Game.