In my estimation, Agent Carter is a lot better than Agents of SHIELD. AOS has only recently shifted out of mediocre territory.
I also prefer Agent Carter, but to be fair I think a lot of that has to do with AoS being beholden to what's currently going on in the movies and now it seems even setting things up for the whole MCU.
Agent Carter on the other hand is pretty much free to do it's own thing and the lower episode per-season count and the smaller cast allows it to tell a more coherent, character focused story.
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