Tiny Toon Adventures/WMG

Elmyra got transferred out of Acme Looniversity after the series ended.
This is the only logical explanation for her being enrolled at Chuck Norris Grammar School in Pinky, Elmyra and the Brain.

Plus, it's easy to imagine the other students at Acme Loo circulating a petition to Principal Bugs Bunny demanding that Elmyra be kicked out of their school.

Elmyra flunked out of Acme Looniversity.
Grammar school is primary education. Looniversity is tertiary. And Elmyra did have the mental capacity of a three-year-old.

Some of the original Looney Tunes shorts took place in Acme Acres.
It's just that it was never mentioned. They happened or were filmed before the Tiny Toons were even born.


 * Impossible, as Buster literally drew that location into existance in the pilot...so, till he was created, Acme Acres didn't exist...

Elmyra is faking it.
Elmyra is Obfuscating Stupidity and is of average intelligence. She's just a sadist.

She is occasionally seen doing sciency stuff. And she wears an animal skull on her bow.
 * Totally exemplified in "The Name Game," in which Elmyra seems to actually trick the bad guys. And Monty is uncharacteristically helpful, which could possibly discredit this, OR open a whole new can of worms.

Gogo Dodo was Demoted to Extra because...
He and Sphinxy from "Sawdust And Toonsil" are a "Item" and were dating long before that episode aired. They also had a baby. Gogo had to take time off from the Looniversity to tend the nest.

Mary Melody was a Real Life girl
That was why she was "The Queen Of Cameos".

Mary Melody is a Badass Normal
This theory is found in some FanFics.

Pinky, Elmyra and the Brain is just a psychotic hallucination.
Elmyra's psychosis was induced by some horrible trauma, probably a number of people dieing or maybe a full-scale disaster in Acme Acres. Monty has the highest chance of being dead, considering his Suspiciously Similar Substitute. Furrball isn't that far behind. She's replacing them in her mind as a coping mechanism.
 * Or someone finally told her she couldn't have pets anymore.

Plucky Duck is an older character than you thought he was.
In the original Looney Tunes short "Quack Shot", Elmer shoots a small green duck. Daffy shows up, takes the little duck from him, bandages it up and puts it back in the water.

Assuming this is Plucky, he naturally considered Daffy his hero, since he saved his life.

Plucky is deliberately imitating Daffy's voice
In the "Baby Plucky" cartoons, Plucky's voice is completely different. After Daffy became Plucky's hero, Plucky decided to be just like him in as many ways as possible.

Furball doesn't speak because he has PTSD
His residences alternate between an alley corner and Elmyra's house, he is a Butt Monkey, and as a Warner Brothers protagonist cat, the universe holds him in special contempt. Is it any wonder he hardly ever speaks?

Calamity Coyote and Lil Beeper are actually siblings
In 'A Piece of Mind' it is shown during a flashback that Calamity and Beeper were delivered by Delivery Stork to the same house (which oddly enough has a Coyote father) the father simply allows the two to play tag. This was what caused Calamity to begin his chase of the roadrunner. It is shown during the flashback that when Calamity moved to the city, he was visbly crying over the fact that there wouldn't be Lil Beeper - until he sees a second moving van and Beeper waving at him. Seeing how Calamity was very young at the age, he most likely didn't know that Beeper was coming with him because he wasn't in the first moving van. This can happen to younger siblings in real life.

It is likely that the fighting is merely extreme Sibling Rivalry as the two are seen at school and other events as perfectly fine with eachother.

Calamity Coyote has Asperger's Syndrome
He fits most of the Asperger traits. With:

Obsession - Catching the Lil Beeper and also machines

Extreme Abilities and Knowledge past his age - Despite having a Vague Age it's hinted that he is one of the youngest of the Toons. One episode opens up with him reading a book on Quantum Physics.

Uncordinated - Some of his mishaps are caused by being clumsy and when he is thinking he is always tapping his foot or walking.

Sensitivity - Of course he reacts greatly to injuries but also reacts to other things differently. Such as being affected by Fifi's stench greater than others, he has very good hearing (notice he always grimaces when Lil Beeper goes Beep Beep near him) and apparently has extreme strength for his age.

Imagination: He can be REALLY creative and almost imposible with his ideas on how to catch Lil Beeper (or on one occasion Buster). Oddly enough he isn't a Cloudcukoo Lander or a Jerkass like many other characters.

Hamton and Furrball also have Asperger's Syndrome
Hamton and Furrball share some of the same Asperger traits as Calamity, including:

Obsession - Hamton's is cleanliness and eating, whereas Furrball's is finding a decent home and/or owner.

Extreme Abilities and Knowledge past his age - Hamton seems to know everything there is about cleaning, whereas Furrball, despite his unknown age, seems to know and fixate on all the little things that happen in his personal life, including the flea family.

Uncoordinated - Both have their share of clumsiness, insecurity, and misfortune whenever their minds are on something or, in Hamton's case, being manipulated by Plucky.

Sensitivity - Though Hamton's obsession with cleanliness still applies to this one as well, he does have his moments where his anger gets the better of him, as well as worry in general. Furrball will jump at anything that excites or frightens him, and in some cases, go after those who annoy him.

Imagination: Hamton has his moments where he's had some ideas in mind in certain episodes that nobody really saw coming, while Furrball can never stop picturing the perfect home for him.

Soul Eater is a revamp of Tiny Toon Adventures
Having matured slightly--and grown tired of being off the air--the characters transferred themselves and their school to Japan and got themselves redrawn into anime characters. Buster and Babs are Soul and Maka, Plucky is Black Star, and Hamton is Death The Kid. Lord Death is, of course, Bugs Bunny.

Pepe is Fifi's maternal uncle.
They have different last names, so he'd have to be related to her mother. When Gigi LePew married Antoine LeFume and had kits, she wanted to name one after her brother. However, the litter turned out to be all girls. Since Pepe is a pet form of Joseph, Gigi named one of her kits Josephine, the pet form being Fifi.