Some new thoughts:
Doktor Tomoe from Sailor Moon became a villian to save his daughters life and Anakin Skywalker became a villian in Revenge of the Sith to save the life of his whife and of his unborn child.
The reason for the actions of Gendo Ikari in Neon Genesis Evangelion was his whife and the reason for the actions of Anakin Skywalker in Revenge of the Sith was Padme Amidala.
In Neon Genesis Evangelion , Yui Ikari disappears and most people believe she is dead, but later it`s revealed that she is in Eva 01 and because of the long life span of Eva 01 , she is nearly immortal. In Star Wars Episode 1 , Qui gon jinn is killed by Darth Maul , but in Episode 3 it`s revealed , that Qui gon found a way to become immortal.
Count Doku reminded me of Char Aznabel from Gundam. Both are one of the main enemies of the hero. Both had many fights against the main character , both are very much like knights and both are very important members of rebellious oranisations. In the End of Mobile Suit Gundam , Char and Amuro fight a sword fight on a space station shortly before the end of a war. In Star Wars Episode 3, Dooku and Anakin fight in a spaceship before the end of a war.
In Gundam , Amuro Rei had an a bit problematic relationship with his boss , Captain Bright Noa and in Star Wars 2 and 3 , Anakin had an a bit problematic relationship with his boss Obi Wan Kenobi.
(The Idea that Anakin build C3PO could have been borrowed from Gundam as well. In Gundam , Amuro Rei buildt a robot called Haro before he became involved with the political incidents. )
In Gundam , Degwin Zabi killed Zeon Zum Daikun to become the new leader of Zeon. In Star Wars , Palpantine tries to make that the Senate elects a new Chancellor to become the ruler of the republic and later , the former Chancellor Valorum became killed by seperatists. Palpantine/ Darth Sidius is the ruler of the seperatists. In Gundam , after Degwin Zabi became the ruler of Zeon , the republic of Zeon became the principality of Zeon. In Star Wars , after Palpantine became the ruler of the Republic , the Republic became the Empire.
In RG Veda , Yasha-oh takes care of the child Ashura, although there is a prophecy which tells that some harmful events will accour if he does it. In Star Wars , Obi Wan Kenobi takes care of the child Anakin ,because of a prophecy although Yoda thinks that because of this , some harmful events will accour.
Because the Jedi knights are a little bit like philosophers and the Jedi temple was a kind of school for Jedi knights , the attack on the Jedi temple could be an allusions of the philosopher school in athens which happens a short time before the beginning of the middle ages, which are also called dark ages of mankind. (I think the time of the rule of the empire was also called a dark age in Star Wars )
Palpantines rise to power has similarities with the rise to power of Augustus in the ancient rome. Both Palpantine and Augustus used tricks to become emperors and after they became rulers , the republics they ruled became empires. The difference between the two is , that Palpantine used special rules to get power and Augustus collected rights to decide things in politics.
The "great jedi purge" could be an allusion to the great purge by Stalin , where Stalin ordered to kill many of his political enemies.
In Ghost in the Shell Innocence , Aramaki , the boss of the heroes sits in his office in front of a big panorama picture , like Palpantine in Episode 3. Both Aramaki and Palpantine are very old persons
According to Wikipedia , the Scene where Anakin walks on the Stairs in front of the Jedi Temple with many clonetroopers was influenced by a scene from the film "The Battleship Potemkin" which is called massacre at the odessa steps.
Here a link to the wikipedia article about the movie "The Battleship Potemkin":
en.wikipedia.org/wiki/The_Battleship_Potemkin#The_Odessa_Steps_sequence
