I actually quite enjoyed the movie, and while I haven't watched it recently, there are still a few gags and scenes that I remember very well:
At the very end of the whole Bart's penis scene, Flanders and his kids are saying grace when Bart smacks into the window right in front of them, and Flanders says "thank the lord for this bountiful-PENIS?!" and the kids repeat "Bountiful penis, amen". My wife repeats this every so often exactly when you would expect.
Homer having a picture of his face taped over Michael Jordan in his wallet.
The whole thing with Bart bonding with Flanders, automatically choking when he thinks Flanders is going to be mad at him, Bart marking up a picture of Homer to look like Flanders and then taunting Homer with it(which I saw as a reference to Matt Groening's original idea to have every person Bart looks up to, like Radioactive Man and Krusty the Clown, resemble Homer).
There's a Flanders line my friend's and family never let die where he says to one of his sons "I wish you didn't have the devil's curly hair." Since I have curly hair I still hear that occasionally.
Bart marking up the wanted poster of the Simpsons family, and the store clerk noticing a ridiculous looking family that perfectly resembles the new wanted poster.
Homer giving double middle fingers as he slowly descends into the sinkhole is a gif I see a lot to this day.
The bomb refusal robot taking a gun and shooting itself from the pressure, mostly because Chief Wiggum's line "he kept talking about it but... I didn't think he'd do it!" Made me laugh.
When Homer and Marge get intimate in the log cabin, and a bunch of Disney style forest creatures help them undress, then react in horror when the act starts.
I'll agree that the writing could have been better and they definitely didn't strike while the iron was hot, but I still have good memories of it and suspect I would enjoy it reasonably well on a rewatch.
Edit: But yeah not having Brooks play Scorpio, and not having Wolfcastle was such a bizarre decision. Tom Hanks cameo was decent though.
Double edit: I just remembered a complaint I had upon first seeing the movie, that the Itchy and Scratchy cartoon that opens the film, while not devoid of humor, felt incredibly tame as far as violence, particularly compared to the stuff they get to do on TV.