Creative Differences: O'Brien was fired at least partly because he was generally a poor musical fit for the band, while Sheppard left Sanctuary and music altogether in 2016 due to general burnout and dissatisfaction with the life of a musician. The departures of Loomis and Williams, meanwhile, were strictly due to their steadily-deteriorating relationship with Dane and Sheppard.
Hitless Hit Album: Inverted. Whilst Dead World WAS a critical success, and well-received by fans, its big single was supposed to be "Believe in Nothing". Keywords here being "supposed to be."
Promoted Fanboy: Attila Voros was a HUGE fan of Nevermore and Jeff Loomis well before he got the job as a live guitarist and had a style that was heavily modeled after Loomis' own; had Nevermore ever reunited, he would have likely been inducted into the band as a full member.
Troubled Production: The Obsidian Conspiracy. The inter-band tensions that started to build during the touring cycle for This Godless Endeavor had reached a boiling point long before they even had the album written, and while Dane and Loomis' solo albums helped them take a much-needed break from Nevermore and kept the band intact, the fact of the matter is that by 2009, the band was firmly split down the middle (Dane/Sheppard and Loomis/Williams). Furthermore, the producer urged Loomis to cut down some of the lengthier tracks that he had wanted to do; the result was a generally disliked album that, in retrospect, was a clear sign of a band that just didn't care any more and was just trying to get an album done so they could meet a deadline.
The Webcomic
What Could Have Been: Red & Flynn's Patreon provides several Behind-The-Scenes posts revealing some things that didn't make it into the finished comic. This includes Deleted Scenes and several noticeably different drafts of episode 1.
Lenore was going to arrive in Nevermore wearing a dress.
Lenore's suitcase was going to be bigger and heavier, requiring her to carry it on her back. The Deans comment that she 'overpacked'.
Nevermore Academy had a few different names, including Edgeside and Brinkside.
Lenore was guided to the Academy by the Raven and/or the glowing orbs, both of which are antagonistic towards the Academy in the published series. Lenore was also nicer to the Raven, calling him 'Master Raven'.
In two of the drafts reveled, Lenore doesn't meet Annabel Lee before entering the Academy. In another, she finds Annabel unconscious and suspended by brambles.
Concept art and early drafts show several early character designs.
The Deans had different distinguishing features, such as one having orange eyes and the other having blue.
Lenore had several different hairstyles in preproduction, and at least one version of her uniform included a skirt.
Annabel Lee's Spectre form had a lantern and translucent skin.
Morella went through several wildly different designs. Her distinctive orange pigtails in particular were a late-stage decision — The behind-the-scenes for episode 4 & 5 even includes full-color panels of Morella with a different hairstyle.
Eulalie was originally going to be a colder, more stoic character with a Yuki Onna Spectre.
Word of Gay: Red has confirmed that Prospero is aromantic.
Word of God: A couple things have been confirmed by the creators on discord.
Lenore and Annabel lived during the Victorian era/Gilded Age.
Morella is around 18-20, and the youngest of the major characters.