I like this idea. I guess the first question is when do you think The Simpsons stopped being good? For me the last great season is 8. But there are some gems in season 9, more than any subsequent season (do to it including some holdover episodes from season 8). Off the top of my head I like the NYC one, ‘Realty Bites’ and ‘Cartridge Family’.
I think it’s important to have a Treehouse episode (you could mix and match the segments from different years). There should also be a Sideshow Bob episode. Not sure which I would pick. And it’s a good idea to get as much Phil Hartman as possible (his last appearance is in season 10).
As for closure, that’s a good point. I think the one where Maude Flanders dies would probably be a good inclusion (even if it’s a little depressing). Also ‘Behind the Laughter’ feels like a final season kind of episode. Not sure how far into the series you want to go, in terms of matching SD/HD episodes, but I vaguely remember there being some decent stuff in season 20 that could give a good sense of finality.
There’s “Holidays of Future Present”, which to my understanding was deemed the ‘canonical’ conclusion to the show out of all the ‘future’ episodes they’ve done, but theree’s also “Barthood”, which I often felt was the more believable ending out of the two.
Sideshow Bob wound up having a family, but that ended up being ignored with subsequent appearances. I always felt like “Brother From Another Series” was the natural ending for Bob’s character, as he does a lot of redeeming things in that episode, he and Bart work together etc. Maybe an alternative ending could be given to that episode as it originally ends with Bob being incarcerated again.
Another idea I had would be to trim half of “Homer’s Enemy” off and join it up with it’s follow-up where his son is out for revenge on Homer and Sideshow Bob helps the family track down the culprit.