0:54 - Yoda: "Luminous beings are we." He also says this in The Empire Strikes Back [1:10:54].
2:43 - Tarkin: "You yourselves [the Jedi] said that you're peacekeepers, not soldiers." In Attack of the Clones, Mace Windu says something similar: "We're keepers of the peace, not soldiers" [4:49].
2:51 - Tarkin (to Ahsoka, after she says she hopes Palpatine knows what he's doing): "I assure you that he rarely does anything without a strategy." Palpatine uses similar expressions talking to Mace Windu and addressing the senate in Revenge of the Sith ("And I assure you, the senate will vote to continue the war as long as Grievous is alive" [25:12] and "But I assure you, my resolve has never been stronger!" [1:35:16]) and talking to Luke in Return of the Jedi ("I assure you we are quite safe from your friends here" [1:32:08]). Qui-Gon also uses the expression in The Phantom Menace; after Queen Amidala says that Senator Palpatine fears the Trade Federation wants to destroy her, he replies, "I assure you I will not allow that to happen" [1:36:33].
16:06 - Anakin (to the clone troopers, referring to Ahsoka): "Set weapons to stun; I want her alive." There are two similarities here. In A New Hope, a stormtrooper aboard the Tantive IV says, "Set for stun" [6:24], and Vader orders the stormtroopers to "bring me the passengers; I want them alive!" [6:08]. He gives similar orders in The Empire Strikes Back; he tells the bounty hunters: "You are free to use any methods necessary, but I want them alive, no disintegrations" [1:06:14] and instructs Admiral Piett: "Prepare the boarding party, and set your weapons for stun" [1:57:09].
20:50 - Anakin (to Ahsoka): "Trust me." Han also says this (to Leia) in The Empire Strikes Back [1:20:06].
21:21 - The shot of Ahsoka jumping into the lower levels has the same basic composition as that of Anakin jumping through the lanes of speeder traffic in Attack of the Clones [19:15]:
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At 10:29, there's a brief cue of the Imperial march when Anakin starts to get angry at Commander Fox for not letting him in to see Ahsoka.