Endgame sections for all the main titles
RBYG: Get to do anything you want & Capture Mewtwo. As a kid this was pretty cool to find and fix stuff you couldn't do.
GSC: Go to Kanto, get lugia and ho-oh after getting the three beasts, and do anything you want.
RSE: Find Latios or Latias, do battle frontier, Find Regis (Even though you can do that anytime I think) and Find Rayquaza, as well as Groudon and Kyogre if you have emerald.
FR&LG: Do the rest of the Sevii Islands, trade with RSE, get mewtwo, and face a harder E4.
DPP: do whatever you want, battle frontier, get legendaries that wern't available for you to get and other pokemon. Harder E4.
SS&HG: Everything from GSC except add in battle frontier, Groudon, Kyogre, and Rayquaza, Latios or Latias, and face Lance and Clair at the same time.
B&W: Do whatever you want, find other legendaries, see new cites, get magikarp, finally face the champion of Unova, also battle Cynthia.
I like second gens and third gens post games more than the others. They did things right for that.