Age of Apostasy- This is a cornerstone event of the modern 40k setting. This is what gave rise to the modern ecclesiarchy and the Sisters of Battle. To see their roots in the Brides of the Emperor and to read tales of Goge Vandire, Sebastian Thor and the Confederation of Light! Plus to have some nice Space Marine and Custodian action on Terra would be pretty sweet. Also, what is nice is most of this is actually conflict between mortals, not demi-gods like HH. To have characters more down to earth again would be welcome (Finish Gaunt's Ghosts already!)This would likely have to be at least the length of The Beast Rises (same monthly format mayhaps) or even larger. But what a tale!
The Fall of the Eldar- Spawned a Chaos God and the Eye of Terror. Caused the Eldar to split into two different main factions and a variety of lesser ones. Lead to the establishment of Aspects and spirit stones. Lead to the existence of Craftworlds. Basically, everything important for this seminal 40k race is established as a result of or during the fall. Some Probably an important event right? To see its build up, occurrence, and immediate aftermath would be quite the spectacle. I imaging 3 to 6 books being enough. If they can do the Macharian crusade in 3, they can do this.
The Unification Wars (Unification of Terra)- Who doesn't like Thunderwarriors? That's right no one. They are awesome. So why not some stories about them vs the Panpacific Empire? Hy Brasil? How cool what it be to read about the pacification of Albyon or the sieges of the hives of Nord Merica. The coolest thing about the potential this has is its relatability to the audience. Imagine sitting at home and all the sudden the book you are ready talks about a battle... IN YOUR CITY! Would be pretty cool in my opinion. Oh, and it would have tons of sweet Emperor action and Malcador intrigue. I would hope for no less than 12 books myself.
The Badab War- The Tale of the Tyrant of Badab and his succession from the Imperium. Largest Space Marine on Space Marine conflict since the Horus Heresy. Already laid out in Imperial Armour, this could easily be done in 10 or less books. There are some really neat characters and a lot of very fluffy but often forgotten space marine chapters too. And tons of really cool moments. And the Space Sharks. Anything with Tyberos the Red Wake is worth doing. It would also be a very easy tie in back to the game. Did you know that the Horus Heresy models actually all started as Badab ones? All the variant MK power armours came from Badab first. So an easy pitch and a reason to release an updated IA book from FW. Easy to do in a few books too, especially since it is all already detailed in 2 Imperial Armour books.
The Abyssal Crusade- One of the worst disasters for the Imperium, it led to the loss of numerous Space Marine chapters, almost all of whom turned renegade as a result. Basically a corrupt (read corrupted) High Lord finds 30 Space Marine Chapters wanting and sends them into the Eye of Terror on a crusade of penance. This is a lie. Begin. The books could follow one over all plot or each document a different chapter and their part of the crusade, probably finishing with a little duology of the Vorpal Swords, following their crusade and retribution. Maybe not follow all 30 chapters, but some of the more notable ones? Include a short story anthology or two for some of the lesser ones?
The Black Crusades- There are 13 of them... for crying out loud why are there not more books about them! A continual driving factor in the 40k universe since the Heresy. As far as I am aware, there are only books about the Gothic War (12th Black Crusade) and even then they aren't a lot and really don't document it (though they are awesome. Best source for the crusade though is the BFG rulebook). But would it be too hard to get a trilogy on each of these, following Abaddon, the ultimate baddie, and his merry band of Chaos Marines? And who doesn't want to read about such conflicts as "The Skullgather", "The Tide of Blood" or "The Ghost War". Neat stuff this 40k, right?
The Tale of Ursarkar E. Creed- A trilogy just waiting to happen. Follow him from Whiteshield to Lord Castellan of Cadia, and all of his heroic battles along the way. Why would you not want to read about this man's tactical genius? He is larger than life and, as I said before, would give us fans another "muggle" to relate to as the central figure of the story.
The Tale of Commander Farsight- Yet ANOTHER trilogy waiting to happen. Follow him from Shas'Saal to Shas'O, and all his heroic battles along the way. Why would you not want to read about this fishperson's tactical genius? He is larger than the Greater Good and, as I said before, would give another "mug.... well I guess not. BUT it wouldn't be more Space Marine Samurai Jacktion now would it. And that is always nice. Plus, understanding such an important figure in a non-core storyline faction would be nice. Especially as the story line moves forward. He most assuredly still has a role to play in the Galaxy. Plus, a renegade Tau with a what is likely a C'tan blade is COOL!
The Sabbat Worlds Crusade- HA, JOKES ON YOU! THEY ARE ALREADY DOING THIS! I just wish Dan Abnett would stop doing Marvel stuff and finish it (and the Pariah Trilogy). Dan, I love Guardians of the Galaxy and all, but really I NEED this. NEEEEEEEED. (This is the Gaunt's Ghosts series for those of you who don't get it.)
Honourable Mention: Night of 1000 Rebellions- So this wouldn't be a series. But it could make for one of the COOOOOLEST short story anthologies they have EVER DONE! Basically a Chaos Superplot and a massive psychic scream cause hundreds, if not thousands, of Imperial Worlds to rebel at the same time. Opportunities for creativity abound.
Did I miss anything BIG!!! Is there something you want to see?