In the earliest days of development, Dr. Crevis was the third most important character in the series, existing even before Libby did.
He was Donnie's therapist, whom he'd unwillingly go see on a regular basis. This was at a time when Donnie didn't wish to receive help for his condition, or at least not through therapy, and there would have been a point at the end of the series where Donnie kills Crevis and reaches a point of no return. Crevis would eventually be scrapped after the series ended up going down a different path.
He was originally meant to have a brief scene in The Masked Stalkee's Last Stand but was cut due to the episode running too long.
While AJ having a brother was an idea early in development, this was not that.
In The Twisted Tale of Terrible Tyrants, Gerald and Ciara mention "life-changing news" that they decide to refuse to tell AJ about and simply have her wait to find out about it. This was originally planned to be a sort of side plot of Ciara being pregnant, with little hints about this being scattered throughout the series up until the second-to-last episode when Clancy would be born. This would result in AJ falling into a deep depression through a series of factors as a result of Clancy's birth and was intended to be the gateway to a spin-off series starring AJ as now a 16-year-old, with Clancy serving as the deuteragonist.
The decision to cut this storyline was actually made just before The Twisted Tale of Terrible Tyrants was released, and while the life-changing news scene was meant to be cut or altered, Brandon struggled to think of a good replacement in time, so it ended up being left in.
The storyline was cut for a multitude of reasons, including the growing unlikelihood of any sort of spin-off, at least for this version of the series. However, what ultimately killed it was simply the fear of a new baby character being introduced at the end of the series seeming like a weird, random move that might make a lot of people upset.
In hindsight though, Brandon believes cutting the storyline was for the best, as he now finds it weird for AJ to fall into a deep depression over some relatively minor incidents compared to what she goes through daily.
There were once brief talks of giving Donnie a little sister. She would have been the fourth sibling of the family and be significantly younger than the others (about 5-7 years old). She was conceptualized as a girly princess-type character and was planned to allow for Donnie to show off his more childish side, with various scenes of the two playing games of pretend with each other. She was a generally shy but playful kid who enjoyed spending time with Donnie and was considered closest to him.
Ultimately, the character would never end up going anywhere. While no concept art was ever drawn, she was imagined as wearing a poofy pink dress with golden locks (likely a wig).