Don't know what you mean by arcs, but I liked the Leonardo and Raphael-centric episodes the most, as they usually learnt something in them. I also liked how April had a more proactive role in the Red Sky seasons.
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Donatello: The tracker! It might work.
*Donatello goes to the back of the Turtle Van*
Raphael: Shrewd move, Donatello. If we ignore the problem, it might go away by itself. (from The Mean Machines)
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