Alert the presses! Shocker of shockers: Series that are Done Well happen to be Good.
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Seriously though, in a post-modern world where all stories have been done before it is always about the "execution". Even bland can be great is you add the right emphasis (or enough boobs, depending on the audience).
As for series that do this well: Princess Nine, Madoka, Kokoro Connect, Ano Hana, and I'm sure quite a few others...