I'm actually going to give them the benefit of the doubt on it being a 'silly little skit'. We can talk about context and additional circumstances all day (easily) but in regards to the skit, let's not read into their relationship. After all, it's a fictional setting-- Lily doesn't actually live with a Gardevoir, or Bonnie, or even Mikaila. It's just a setup for Mikaila to discuss a comic while Bonnie provides her own cheeky commentary.
Instead, let's discuss why the joke is so terrible people are immediately jumping to this conclusion. Because it's such a terrible joke that the only conclusion is that the punchline is 'emotional neglect (??)'.
Whichever of them wrote this sketch, they can't tell a joke. They took a setup that on its own isn't really supposed to be funny ("Honey, I don't read comics") and then stitched it with a joke about the other character making an excuse to avoid an obligation and running away. The former could be written as:
L; "Honey, I don't read comics."
M: "Oh..." /sad pose
/pause for consideration
L: "But I know who dooooes~"
/cue Bonnie rising from the counter
Not a great joke, but at least it follows through. You could also have a joke about "Sorry, Mik, G and I were going to <engage in comical activity>", which still gives you a bit of a punchline while also making Lily's departure accidental.
The latter, meanwhile, is usually also fitted with a comical excuse for leaving. "I have to go... wash my hair!" says the bald character as he flees the scene. Lily isn't offering a comically obvious (or comically complex) excuse, she just says "I'm gonna go hang out with G" and then runs like she's pretending she has an obligation. Mikaila wasn't being particularly pushy and so Lily's response reads as not only petty but disproportionate, making it seem less like she's fleeing the obligation and more that she's just fleeing Mikaila, because the writer didn't understand HOW this setup is supposed to work.
This would make more sense if maybe Mikaila had gone to everybody else in the house and they were all busy with progressively sillier tasks before returning to the kitchen and then Bonnie shows up. It would require a lot more work (and more than two characters) but I'm really just spitballing for how this joke could have possibly landed.
So the only conclusion the audience can reach is that the joke is that Lily is so desperate to avoid letting Mikaila share something she enjoyed that she'd rather flee the scene to spend time with her abusive psychopath of a Pokemon-- that somehow THAT is what's innately funny here.