The title of this episode comes from a line in the opening crawl of Revenge of the Sith: "There are heroes on both sides."
5:12 - Padmé: "If only I could talk to Senator Bonteri."
Ashoka: "Who's he?"
Padmé: "He is a she. A senator in the Confederacy of Independent Systems."
This is the same sort of confusion that Obi-Wan and Anakin experience with Zam Wesell in Attack of the Clones. Anakin explains: "I think he is a she, and I think she's a changeling." [22:28].
5:44 - Ahsoka: "Well, Master Skywalker and I hold what we call 'aggressive negotiations' all the time." In Attack of the Clones, Anakin says to Padmé: "And when I got to them, we went into aggressive negotiations" [53:01], which he explains means "negotiations with a lightsaber." Padmé also uses the phrase later: "I call it aggressive negotiations" [1:54:08].
8:06 - Battle droid: "Move along, please. Move along." In A New Hope, a sandtrooper has a similar line when, prompted by Obi-Wan's influence through the Force, he directs Luke into Mos Eisley: "Move along. Move along." [43:51].
8:26 - Mina Bonteri (to Padmé): "Hello, old friend." She also calls her "my old friend" a bit later [12:25]. Perhaps coincidentally, this same phrase is applied to Obi-Wan in Attack of the Clones when Palpatine suggests him as protection for Padmé: "an old friend, like Master Kenobi" [6:34]. Count Dooku also uses the phrase when he calls Mace Windu "my old Jedi friend" [1:50:24] and just "old friend" [1:56:05]. In Revenge of the Sith Obi-Wan says, "Goodbye, old friend" to Anakin as he leaves for Utapau [51:13], and Yoda refers to Qui-Gon as "an old friend" [2:09:56]. In A New Hope, Leia uses the phrase sarcastically to refer to stormtroopers when she says that she and Luke "ran into some old friends" [1:31:33]; in The Empire Strikes Back Yoda says that through the Force, Luke will see "Old friends long gone" [1:17:05]; and in Return of the Jedi Luke says, "I have a promise to keep to an old friend" [37:37], and Han calls C-3PO "an old friend of mine" [1:11:53].
13:18 - Visually, the Separatist Parliament seems to have been inspired by the British House of Commons:
20:27 - Padmé (about Mas Amedda's claim that the Separatists offered peace negotiations as a tactic to get the Republic to lower its defenses): "No, that's not true." Luke has a similar line in The Empire Strikes Back when Vader tells him about his father: "That's not true. That's impossible." [1:51:21].