1:37 - Obi-Wan (to Chairman Cho): "With all due respect Chairman, this is for the senate to decide, not us." In The Phantom Menace, Qui-Gon and Obi-Wan's pilot uses the same expression ("With all due respect, the ambassadors for the Supreme Chancellor wish to board immediately" [2:06]), and Obi-Wan uses it in Revenge of the Sith while speaking to Mace Windu about Anakin ("With all due respect, Master, is he not the chosen one?" [40:32]).
4:04 - Anakin (to Obi-Wan): "Sensors are in place." Han Solo says something similar in The Empire Strikes Back: "Sensors are placed" [3:45].
4:08 - Obi-Wan (when the hologram project doesn't work): "Blast it!" He also says "Blast!" when Jango Fett ambushes him in Attack of the Clones ("Blast! This is why I hate flying!" [1:08:22]), and Luke says it twice in A New Hope: after R2-D2 disappears ("Blast it!" [26:49]) and when a TIE fighter is behind him during the Battle of Yavin ("Blast it, Biggs, where are you?" [1:49:09]).
4:10 - Anakins hits a hologram projector in order to get it working again, just like Han Solo does with the Millennium Falcon in The Empire Strikes Back [35:07].
4:12 - Battle droid (in a hologram recording): "685 to command. There're too many of them." Captain Panaka says something similar in The Phantom Menace (referring to battle droids): "There are too many of them" [23:25], as does a Jedi youngling in Revenge of the Sith (referring to the clones executing Order 66 at the Jedi temple): "Master Skywalker, there are too many of them" [1:23:40], and a rebel pilot says basically the same thing in Return of the Jedi (referring to TIE fighters): "There's too many of them" [1:35:13].
6:36 - Two Talz cross their spears in front of Anakin and Obi-Wan, just as two Gamorrean guards do in front of Luke in Return of the Jedi [22:33]:
6:53 - Obi-Wan (after Anakin asks how he's going to communicate with the Talz): "Patience. Maybe they're smarter than we are." It's unclear whether "Patience" is his answer to Anakin's question or merely his advice, but in The Empire Strikes Back, Yoda and Obi-Wan also counsel Luke with, "Patience!" [Yoda at 54:36 and 55:03; Obi-Wan at 1:24:18], and in Return of the Jedi, the Emperor advises Vader: "Patience, my friend" [38:57]. It's also part of Obi-Wan's advice to Anakin in Attack of the Clones: "Patience. Use the Force. Think." [21:49]. Also in Attack of the Clones, Dooku, referring to Padmé, tells Gunray, "Patience, Viceroy, patience; she will die" [1:49:27].
8:16 - Anakin (after Rex comments about the weather): "You don't know the half of it." He also uses this expression while talking to Kitster in The Phantom Menace: "That isn't the half of it" [47:59] and then goes on to explain that he's going to be in the podrace.
11:51 - Chairman Cho (after Senator Chuchi offers to represent Pantora): "Not on your life, Senator. There will be no diplomacy this time." There are similarities here to two lines in A New Hope. After a rebel technician offers Luke a new droid to replace R2, he replies, "Not on your life" [1:43:43], and after Vader gives order to retrieve the escape pod, he says, "There'll be no one to stop us this time" [8:44].
13:59 - Rex (after Chairman Cho orders him to fire on the Talz): "Sir, with all due respect, we're only here to protect you." See above, 1:37.
14:11 - Chairman Cho: "It's a trap!" Admiral Ackbar is famous for saying this in Return of the Jedi [1:35:03], but Leia says this to Luke (twice!) in The Empire Strikes Back [1:39:50].
19:03 - Obi-Wan (urging Senator Chuchi to negotiate with the Talz): "Senator, now is the time." The situation is quite different, but while speaking to Tion Medon in Revenge of the Sith, he says something similar: "If you have warriors, now is the time" [55:19].
21:14 - Anakin (to Senator Chuchi): "Yes, most impressive." Vader gives a similar compliment to Luke in The Empire Strikes Back: "Impressive, most impressive" [1:44:30].
21:38 - Senator Chuchi (after Obi-Wan tells her to make the peace last and set an example): "I will, I promise you." In The Phantom Menace, Obi-Wan tells Anakin, "You will be a Jedi, I promise" [2:07:43], and in Revenge of the Sith, Padmé tells Anakin, "I'm not gonna die in childbirth, Ani, I promise you," and he replies, "No, I promise you" [53:46].
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The clone troopers' cold weather gear is based on a Ralph McQuarrie concept painting of snowtroopers for The Empire Strikes Back. Captain Rex's helmet even includes the same symbol on the side:
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