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Other than Thousand Sons, I'm satisfied with most of the Traitor Legion rules. This is more about tweaking some things here and there without going overboard.

Black Legion: No complaints here actually, as most the relics at least have some use. Maybe make Gift of Balefire AP 2 (it's a one-use shot after all) or so but other than that, not too much to complain about.

Alpha Legion:
Modify Forward Agents to allow Infantry ICs that are not in Terminator Armor to Infiltrate.
Replace the Forward Operative Warlord Trait with:
Headhunter: The Warlord and his unit have the Precision Shots special rule.

Redo Faceless Commander as follows:
Roll for a Personal or Command Warlord Trait. Your Warlord has this Warlord Trait As long as the Warlord is alive, then at the start of each turn, your Warlord may choose another character to use that Personal Warlord Trait instead of him.
Add the following to Alpha Strategist: Additionally, if the Warlord starts starts his turn within 6" of a table edge, any Alpha Legion unit that Out flanks may choose to arrive from that table edge (this may even be your opponent's Table Edge), so long as the unit ends up entirely within 12" of the Warlord (basically a more restrictive Positional Relay).
Otherwise, ths ability is useless if you wish to start on the table or gain a new Warlord from Many Heads of the Hydra.

Iron Warriors:
Allow Iron Within, Iron Without to stack with other FNP sources. Can't let the Iron Hands have all the fun.

Redo the Cold Calculations Warlord Trait as follows: When a friendly Iron Warriors unit within 6" of the Warlord fires blast weapons against an enemy unit that is within 6" of another friendly Iron Warriors unit, you roll 3d6 for scatter and drop the highest die.

Warpbreacher: Increase to 30 points. The Warpbreacher grants the vehicle Power of the Machine Spirit instead of Possession.
Nest of Mechaserpents: 25 points. The Warpsmith ignores the Unwieldy special rule, and all his melee attacks have the Swiftstrike special rule. Go Doc Oc on your opponents.

Night Lords:
Modify In Midnight Clad as follows:
If that unit already had Fear, enemy units take Fear tests against that unit on 3d6 dice, dropping the lowest die. That way, Raptors still remain relevant-ish Fearwise, compared to Night Lord Bikes.
Modify Terror Tactics to be a -1 Leadership Penalty to all Morale, Fear, or Pinning checks caused by Night Lords. That way you can have fun doing stuff like tank-shocking, pinning Marines that lose their Razorbacks, etc.

Word Bearers:
Unexpected Boon: May choose a free Boon, except for Spawndom, Multiple Boons, or Dark Apotheosis.

Add the following to Profane Zeal: The Dark Apostle's Beseech the Chaos Gods ability to re-roll Chaos Boons affects both his own unit, and any characters in any unit within 6" of him.

Redo Unholy Pact as follows:
Possessed are Troops. Any Word Bearers units with the Daemon USR may Run and Charge (hello Maulerfiends! Note, Mutilators/Obliterators would still not be able to run due to Slow and Purposeful). Word Bearers Psykers harness Warp Charge points on a 3+ when attempting to manifest powers from the Daemonology (Malefic) Discipline.

World Eaters:
Replace the Furious Charge bonus with +1 Attack base. Replace the Butcherhorde's ability to re-roll charges with the ability to Run & Charge starting from turn 2. Suddenly, there's now a reason to take the Maelstrom of Gore over a Warband.

Death Guard:
All good here, boss. Maybe FNP 4+ base for the Plagues themselves so they're not overshadowed by the Relentless autohavocs?

Emperor's Children:
Remove the "before it has made any attacks" qualifier from Fuelled By Sensation. With their Initiative, there are very few units that will strike before your guys anyway, regulating this to Obliterators and Meltabombs or so.
Remove the +1 Initiative Combat Drugs result, shift the results, and make 6 "Choose".
Quicksilver Reflexes grants Hit&Run rather than +2 Initiative.
Psychotropic Aura is redone as follows: Friendly Emperor's Children units firing at an enemy unit within 6" of the Warlord add +1 shots to the profiles of any Sonic Weapons.

Thousand Sons:
This requires another thread altogether. These guys are a mess. (In b4 "...but Magnus")