I have to vote for the original series on principle.
But Mystery Incorporated is absolutely excellent television in every respect. Its not just a great Scooby-Doo show, its a great show that has the twists and turns that you'd expect in a major network show. Its phenomenal.
The original will always have a special place in my heart because it's what brought us Scooby-Doo but I have to go with Mystery Incorporated because it showed us that Scooby-Doo could be more then just bad guys in masks