Summary by @tldr:

Each one pulls the story in a different direction, but their collective tilt equals out to zero, resulting in a show that always manages to stay on course and feel well rounded, allowing it to cater to almost every taste.
Scooby-Doo: Mystery Incorporated is a serially progressing story with self-contained episodes, meaning that each individual caper is fun to watch, but you get maximum enjoyment by viewing them all in order from start to finish.
This series takes inspiration from many of the great mystery shows of the past few decades, including Twin Peaks and The X-Files and even has the odd reference here and there to provide an homage to these predecessors.
For the first time in the franchise's history, the heroes are set against an equally worthy group of villains, who present a real challenge and who often have the upper hand.
Scooby-Doo: Mystery Incorporated takes place in the fictional town of Crystal Cove, a small American borough with an active criminal population due to rumors of an ancient treasure that exist somewhere inside the city limits.
This show did what Thundercats and Transformers failed to do: present us with a remake that not only exceeded the original, but gave fresh justification to the entire IPs existence.
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