My ideas on this:
The different chapters: this will probably be like DW, 12 or so skills+talents cheaper/only avaiable to a single chapter, 12 or so to another, etc... The "newbies" could use their parent table, changing some skills or talents for others more chaos-related.
Following on the Deatwatch style of Space Marines, it is likely they will have the following tables: 1) chapter table, 2) chaos god table (5 tables here: one per god, and a fifth for Chaos Undivided), 3) specialty table. While it is possible that certain alternative advancements (like Noise Marine) will require to be a member of a certain Legion, remember you can be "sold" to a Legion, at least according to the Dawn of War storyline (Eliphas the Inheritor was a Word Bearer in DoW: Dark Crusade, to be sold to Abaddon and become a Black Legion member in Chaos Rising).
For the traitor legions previously discussed:
First, the Thousand Sons: this ones will most likely be avaiable only as sorcerers. The animated suits of armor always obey a Thousand Sons sorcerer, and that is a ***** for a player, even if the armors can go on their own. I think recruiting Rubric Marines as minions will be cheaper for these characters aswell.
Second, the Alpha Legion: I see some problems with them being in this supplement, as far as I know no member of the Alpha Legion has ever been in the Warp without the protection of a Geller Field (and no, they never went inside the Eye of Terror). Furthermore, they are not mutated, and they don't serve any chaos god...
The World Eaters would be another option to have as minions, since, well, I think most (if not all) of them are just crazy killing machines (specially their Daemon Primarch).
For the FFG "Chaos Legion", it should be a post-heresy traitor chapter, since I doubt Games Workshop will allow the use of one of the two "free slots" in their count of 20 original primarchs/legions. As for the other ones, I have no comment there ^^