When I was a small child, I encountered the very first version of Scooby-Doo, namely Scooby-Doo, Where Are You! [sic}(1969-71), and watched it faithfully. As I got older, of course, I outgrew the series. The action was silly, the plots repetitive, the humor pure formula, and the characters dull and unbelievable.
The series remained popular and became a "franchise," with numerous revivals, including made-for-TV movies. Some of the revivals were interesting -- especially movies such as Scooby-Doo on Zombie Island -- but all failed in that none managed to establish believable characters against a consistent background. The series, precisely because of its popularity and hence value to corporate types who wouldn't have known good from bad writing, or cared if they did, would in any case be repeatedly rebooted and the premises changed each time to match the suits' delusions as to what made it fun or relevant.
I had long ago lost hope in the series: I think it may have been Scrappy who killed it for me, and the occasional good movies weren't enough to persuade me to invest any interest in the concept as a whole.
Then I saw Scooby-Doo! Mystery Incorporated. And I was hooked.
To begin with, the 52-episode series has a strong overall plot. Some segments are purely episodic, but as a whole the story is serial: the town of Crystal Cove has a Dark Secret and a Big Bad whose nature is gradually revealed, and the confrontation is (in a three-episode grand finale) quite thoroughly resolved.
The setting is consistent and well-explored. Locations and characters referenced or shown in one story will still be there in the next. It is obvious that the animators were working from a map and an extensive "bible." This makes the events seem real even when they are utterly absurd.
The characterization is very strong. The five main characters (Fred, Daphne, Velma, Shaggy and Scooby) all have complex motivations, act on them, and change their minds and characters appropriately in response to events. They are still first and foremost True Companions, but they have opinions of each other beyond this, including both positive ones (friendship, romantic love) and negative ones (resentment, jealousy). At one point the stresses become so great that the team is torn apart. And these emotional complications are not an afterthought -- they have great significance both to theme and plot.
The main characters are strongly grounded in their world. They have families, and relationships with those families of varying degrees of functionality (this becomes very important to the plot, in ways that would be major spoilers if described in detail). They don't have any strong friendships outside of the Gang (and there's a reason in-story for this which eventually becomes plain) but they do have some friends. They go to school. They interact with other local characters in various ways, even outside of mysteries.
The secondary characterization is also very strong, and secondary characters often have their own story arcs and character development. I will never forget Sheriff Bronson Stone, Janet Nettles, Marcie Fleach, Angel Dynamite, Mr. E, or Professor Pericles, to name the ones who most touched my heart (chilling or warming it, sometimes both). Some of these are friends, some are enemies, and some start as one and become another as the story progresses.
The theme? I'd say it's about the value of true friendship (which can sometimes also be True Love) and the vital importance of staying true to your real self no matter how great the pressures to live a lie. Otherwise you could lose your life -- and soul. Literally.
Oh, and did I mention that it's ultimately a Cosmic Horror story about a Mind Raping, Reality Warping Eldritch Abomination?
No, really. It is.
Good guys win in the end, sort of, but it still is.
You can find the whole series here. I highly-recommend it, even for people who think they don't like Scooby-Doo.
Spoiler comments are just fine.