Kid vs. Kat/WMG

Mrs. Burtonburger is not dead, she's in an asylum.
She is suffering from an extreme case of delirious paranoia, and sees evil aliens everywhere. Her condition is so serious that the Doctors have advised Mr. Burtonburger to keep her away from their children. This is why he never talks about her. Now here is Coop's dilemma: When he keeps claiming that the family's pet is an evil alien, Mr. Burtonburger thinks it means that he is inheriting his mother's insanity. So he does take Coop seriously, but for the wrong reasons.

Kat's a girl
Seriously, in some shots, it looks like it has some... "Talent" on its chest. Unless, that's how all the male aliens of its race looks like, than ewwww.

Kat's one of the missing experiments
They have the same beady black eyes.

Alternatively, Kid vs. Kat is Invader Zim told by an Unreliable Narrator

 * ...makes sense to me.
 * Alternate theory: They take place in the same universe. Zim's superiors are well aware the cats are trying to take over, but send Zim anyway just to get him out of the way.

Kat is not an alien.
He/she is just a normal cat. Coop is a sociopathic child who enjoys torturing animals, and invents the alien story as an excuse. Of course, the series is told from Coop's perspective.

Fiona is a Mary Sue that escaped from a fanfic.
Hmm, she's related to a major character, Coop almost instantly loves her, she's able to break out of Munson's high-tech house, save Coop, learn that Mr. Kat is evil almost right away, and shares quite a few interests in him?

Mrs. Burtonburger was a Munson.
Mr. Burtonburger mentioned loving a Munson but couldn't be with her (or something, I missed a bit of it). He eventually won her over and married her, having Coop and Millie. Whatever happened to her is not so important. But Mrs. Munson hates all the Burtonburgers except for Millie, because she looks like her dead relative.

If there's a season 3, it will be revealed that
Seriously, the fact that, then why NOT   as WELL?

Cats weren't always evil on his homeplanet. Or they tried to be good, but it didn't last because it's not in their nature.
At least one cat is good, and is considered an outsider or a "throwback".

Mrs. Burtonburger is actually working against the various alien invaders, like the Kats and the Hamsters, but in secret.
Her husband thinks that she heartlessly abandoned them, but she actually discovered the danger the Earth is in, and covertly works every day to prevent even more aliens from assuming control over our planet. She's the reason Coop and Millie are so effortlessly skilled at everything they do, as she is a super-spy who is single-handedly protecting Earth. As Mr. Cheeks said: "We're everywhere!", so it would stand to reason that someone has been stopping them from taking over by now, (Because we KNOW it's not because of Agent Napolitan and his ilk) and Mrs. Burtonburger could potentially be this mysterious force.