Season 5 has the Onderon story line which sets up Saw Guerrara (sp?) and introduces him and makes his appearance in Rebels and Rogue one more meaningful. There's the Madalorian storyline that links nicely to rebels as well as the really well done Asoka season ending storyline.
Season 5 was strong except for without giving anything away a middle story line that's awful except you get the introduction to Gregor from Rebels, and he's awesome, he's not just a Clone Trooper he's an ARC and the battle scene with him in my mind was awesome.
The secret to Clone wars is realizing that there are some really bad story arcs, but some really unbelievable story arcs. For me Season 4 was the strongest season for story arcs.
You had
Umbara - which was so incredibly dark, and it makes you understand why most of the troopers even with the chips didn't feel too badly about killing off the Jedi.
The Obi-Wan undercover arc - Which really planted a lot of seeds for Anakin's dissatisfaction and distrust of the order.
Season three
Had the outstanding arc with the origins of most of the Clone troopers that became prevalent in the series.
The Mortis arc which is essential to rebels
The citadel arc where you meet Commander Tarkin and see why he and Vader worked together so well.
And the arc where Asoka gets captured and hunted by the Trandoshians and becomes the jedi that you see in Rebels
Not all arcs are great, but the ones that are are amazing and even the one off episodes are solid. Also when you see these characters in rebels its like meeting an old friend.
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My name is Ozymandias, King of Kings;
Look on my Works, ye Mighty, and despair!
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