Since Scooby-Doo! Mystery Incorporated is done, I thought of creating a poll to everyone to decide which season was the best. Reasons for that decision would be nice, too.
I think both seasons of the show are great.
Season 1 had lead our heroes to learning about the legend of the Original Mystery, Inc. which includes Ricky Owens, Brad Chiles, Cassidy Williams, Judy Reeves, and Professor Pericles. It even introduces new characters to the series like Mayor Jones (until Episode 26) Sheriff Broson Stone, Hot Dog Water, Angel Dynamite (later revealed to be Cassidy Williams), and even some new monsters/villains like Mary-Ann Gleardon as Que Horrifico (later reformed herself in Season 2), Alice May as the Ghost Girl, etc. The returning characters to make their Mystery Incorporated debut are the Hex Girls from Witch's Ghost and Vincent Van Ghoul from 13 Ghosts. However, the downsides to the show include Shaggy being pressured into choosing if he'd rather be with either Velma or Scooby, Fred letting his trap obsession go to his head and not being too focused on Daphne, and the break-up in the finale. But Scooby, being the ever faithful canine he is, vows to get his friends back together. The best Season 1 episodes I've seen are Revenge of the Man Crab, Legend of Alice May, Mystery Solvers State Club Finals, and Night Fright.
Season 2 not only had Scooby keeping his word but also gives the Planispheric Disc a major arc. Also, new characters appearing in the second season are Janet Nettles, the new Crystal Cove mayor, and Nova (Scooby's love life). Not to mention new monsters/villains like Baylor Hotner as the Crybaby Clown, Horbert Feist as the Dreamweaver, and both Gary and Ethan as Hebediah Grim. The main villains are none other than Mr. E (though he would reform), Brad, Judy, and Pericles. As episodes progress, the gang learns about Nibiru, Anunnaki, and the old mystery groups before them. Things become more worse than better, especially when Pericles uses the Planispheric Disk to release the master, known as the Evil Entity. The gang makes a last-ditch effort to eradicate the Evil Entity. After that has been done, they find themselves in Crystal Cove which is now the "Sunniest Place on Earth". The gang finds out they created a new timeline. Sadly, that new timeline means no mysteries are there to be solved. But then, their luck changes when Harlan Ellison, the new Mr. E, tell them he knows what they have done. As the gang drives away, Nova thanks Scooby and the gang. The best Season 2 episodes I've seen are The Night the Clown Cried Part 2, Grim Judgement, Wrath of the Krampus, Dance of the Undead, Nightmare in Red, and Come Undone.
Overall, Mystery Incorporated was, without a doubt, one of the best installments in the Scooby-Doo! saga. Credit goes to Derrick Wyatt for making it all possible.
Those are my thoughts. Let's hear yours.