The secret societies aren't too bad, it's more about the mystery of their true goals.
Sons of Honor: Wants to bring the Voidbringers back (maybe) in order to bring back the good of men. Of course, bad people serve the group, because ends justify means. Members include Brightlord Amaram.
Ghostbloods: Led by some guy named Thaidakar who Gavilar knew about. Shallan's brother was part of their group, and he was probably blackmailing her father. Kasbal and Tyn wanted Jasnah Kholin dead. They are opposed to the Sons of Honor. Don't know their real purpose.
The Diagram: Led at times by King Taravignian with a lot of help from Lieutenants. Focused on a genius plan to destroy and recreate the political landscape to save Roshar. Ends justify the means again. Unknown if the other two societies know of them, but Moash and Graves ended up working for them.
I personally loved the Jasnah appeared right at the end. I went through about 1/2 of the book thinking she was going to get ressed in a lame way and then she just teleports near Wit for a quickie appearance. I imagine every book will have an epilogue where Wit waxes about humanity only for someone to show up unexpectedly. If I were a more inquisitive reader though, I would have seen it coming. Jasna had stated that she and Shallan were of different orders, so the only other order with Soulcasting is the Elsecallers and their other surgebinding is of course Elsecalling. Which basically means Jasnah can travel to Shadesmar in the flesh, and not via cognition like Shallan. I imagine a reread of the prologue has some subtle clues about how Jasnah actually leaves the Material Plane.
I also imagine every book is going to have a prologue with a different POV about Gavilar's assassination. I imagine Adolin/Elhokar/Navani/Aesudan/Eshonai/King Taravingian/Gavilar will be POV's.
Couple corrections I wanted to point out, since I'm anal.
Sons of Honor: Their goals aren't spelled out, but you can infer a lot from this. What they're after is Vorin (and by extension, Alethi) dominance, obtained from the Heralds. To get that sanction, they felt they had to put the world into a crisis sufficient enough to have the Heralds return to Roshar to respond to it. As their plan involved the return of the Listeners' gods (return of the Voidbringers), Gavilar was assassinated. It seemed implied to me that Gavilar was the head of this (and succeeded by Restares). Another inference you can draw, is that Gavilar took the visions he got from the Stormfather -- the same ones his brother was receiving --in a completely different direction, by conspiring to become head of possibly church and state both; to "become the king of everything". (More on the Diagram below.)
Ghostbloods: Shallan's brother might not have been part of this group (I have to dig up the quotes again to be sure). He was bonded with a spren that gave him the same powers as a Skybreaker (see Taravangian's viewpoint), so presumably he found Nin/Nalan and become inducted into that sect.
The Diagram: As you basically said, a terrorist cell, but I got the impression that Gavilar was involved in it as well, if not jointly running it with him. It's very clear that Taravangian and Gavilar have been conspiring together to some extent. The one thing I'm not certain about is the timing of the "Day of the Diagram" with when Gavilar received his visions. Also, reading between the lines: they set Szeth up as a patsy from the start, including his being cast out as Truthless and getting the Windrunner Honorblade as part of that. They wanted an 'unstoppable' force to do their political dirtywork. I'm also very curious to know how Taravangian knows about Jasnah's powers, as well as Helaran Davar receiving his. Likely it's from his nigh-clairvoyant intellect. My personal theory is that on the day he did the Diagram, he received basically a snapshot of the entire world at that moment of time, and his obscene intellect let him predict the course of the future based on that massive dump of information.
Book 3: My money is on the focus being Dalinar, as far as flashbacks go, with Renarin and Jasnah tied for second. Jasnah would be the much more interesting choice, for me, given that we know so little about her progression with Ivory and as an Elsecaller, not to mention what other secrets she found out in Shadesmar that don't apply anymore.
