I will start by saying this, I am not at all a fan of previous Scooby-Doo TV shows, and one of the biggest "complaints" I have heard about this show is that it isn't like the previous shows. In my opinion that is a good thing, it dares to break free from the former chain of reboots that are all the exact same episode after episode. So if you were a die hard fan of the original Scooby show when you were a kid, then this show may not be for you. Please do not form an opinion one thing just because it isn't like something else, that is not an opinion.
Okay, now on to my actual thoughts on the show. Mystery Incorporated immediately changes up the Scooby-Doo formula by having an ongoing plot from episode to episode. You might be able to watch the first half of season 1 with no context but when watching the second half of S1 and most of S2 you will need prior knowledge to understand what is going on. This not only brings the story a serious feeling, (the show has some really dark undertones and themes) but gives opportunities to create new characters never before seen in the Scooby-Doo franchise. The original 5 are still here slightly more likable than before but mostly the same. The original 5 help show off the new characters, and the new characters are great in my opinion. Mr. E, Angel, Sheriff Stone, Hot Dog Water, Brad and Judy, Mayor Jones, Vincent Van Ghoul, Skipper, and especially Professor Pericles all feel so natural in this world. Plus constant recurring characters that will come back later because they have some sort of importance. The writing of the show show is good for the most part but it can have its kind of awkward moments with an overused joke or two. Another reason I love this show as a Scooby-Doo show is because of the plot. The plot of this show (Late S2 especially) is so complicated and twisted just to explain why Scooby can talk. I think this works really well in ways and poorly in other ways.
Now what do I not like about this show. In many cases the animation can look odd. When moving 3D models are used against the 2D characters the overall look feels very unpolished. The animation doesn't look odd at all times just once maybe every 5 or 6 episodes. My other problem would have to be sometimes it's tone is all over the place. For example when nova starts talking about her ancestors it's a little challenging to take seriously. I don't think these problems at all ruin the entirety of the show though.
In all Scooby-Doo Mystery Incorporated is, in my opinion, the best Scooby show out there. With a good story, good characters, and breaking free from 10+ shows before it that all followed the exact same formula every single episode, this show is well worth a watch.
