I've seen the show's 3rd season and the last 2 trilogy stories and I have this to say:
1. Heroes on Both sides:
a. Senator Bonteri said that some Separatists think badly of the Jedi. But Dooku is a Jedi.
b. After all that touching sentiment about ending the war peacefully and boom, the chance is gone and Senator Bonteri is dead?
2. The Nightsisters Trilogy:
a. Ventress was fiercely loyal to Dooku, but that one incident makes her hate his guts?
b. Ventress wanted more power after her Jedi master was killed, so she became an enemy to all Jedi and now hates them?
c. Dooku admires Darth Maul, but he was supposed to be his replacement
d. After fighting to protect his "brother" Savage ended up killing him?
e. Dooku didn't want to kill Ventress in the first place, yet he orders Savage to kill her and gladly attempts to do the deed himself.
f. Mother Talzin helped Savage to help Ventress, yet now she's helping Ventress' newest enemy?
g. It's a little ironic for Anakin to get mad about what Savage did, considering he'll do the same ten fold.
3. The Mortis Trilogy:
a. Considering what Anakin will become, does that mean Qui Gonn was wrong about him?
b. Since we see Ahsoka as an adult, she must survive the war after all
c. After what he saw Anakin become, does Obi-wan honestly still think there is good in Anakin? The darkness within him is strong.
Based on all of this, things just don't add up!