I'm no great fan of Secret War, but it doesn't piss me off like Lisa the Simpson does. The argument that it's a meta-commentary about the show's decline just doesn't wash when there's no self-referential gestures in the episode itself to indicate that (unlike the continuity nods in Homer's Enemy, the writer's room in the Poochie episode, etc. I have a similar issue with Principal and the Pauper, though I mildly like that episode better than some.) Even if it is somehow a meta-commentary and Oakley & Weinstein's warning to Mike Scully, as some have theorized, it simply doesn't work due to its convoluted and contrived nature.
The Simpson Gene is a borderline, dare I say, eugenicist premise that cheapens our understanding of both Homer and Bart as characters. Homer can't simply a schlubby everyman failed by society, he has to some midichlorians-like gimmick to "explain" his stupidity. Bart meanwhile isn't even that stupid, as it has been established that despite being book-dumb he has street smarts - a certain level of cunning or craftiness, if you will - and he'd sure as hell be above unthinkingly eating melted chocolate off the floor like a pig. Episodes like Bart the Genius that suggest he is an outside-the-box thinker who simply doesn't fit society's view of what "smart" is feel more complex and challenging to me.
The conclusion of the episode is simply a ludicrous contrivance. What are we to make of the comment at the end that the "defective Simpson gene is on the Y chromosome, so only men are affected"? Forget the fact that the scene is a blatant exposition dump, scored to treacly music, and that this woman who we've never seen before and will never see again somehow conveniently knows that much about the gene - Lisa's gender didn't even come up as part of her internal conflict for the majority of the episode, but now she's saved from stupidity because of it? Hooray, women are smart and men are stupid? Is that what the episode was about? Lisa remains ashamed of Homer and Bart at the end, only embracing her father because of the Simpson gene, leaving their earlier tiff unsatisfyingly resolved. Homer and Bart's angered response to Lisa's outburst that she doesn't want to turn out like them is perfectly understandable, and yet Goldreyer's script paints them as villains anyway. Had the episode's sympathy been split more evenly between the Simpsons, the conflict might have felt more natural, but much of the episode's focus have been so Lisa-centric (other than the Frostilicus stuff, largely extraneous), and Homer and Bart's characterization so facile and one-dimensional, that this attempt at a "heartwarming" moment is shallow and unearned.
Give me the ending to Lisa's Wedding over this any day - in that one, Lisa decides she loves her father for who he is, and not because of some implausible genetic defect he has that will absolutely guarantee success for her no matter what.
Don't always agree with Dennis Perkins, but his review is worth reading:
https://www.avclub.com/lisa-fears-she-s-slipping-on-a-simpsons-in-fact-slipp-1798185654
EDIT: Probably should've posted this in the R&R thread for Lisa the Simpson, huh? Ah well. Guess I should say a quick word on Secret War, but I spent most of my energy writing the above paragraphs, so I'll just link to
TheRealJims' review instead.