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Personally, and this probably doesn't really meet your criteria, I think that there would be a great story potential in simply where the survivors went directly after Sunnydale. Season 8 in the comics starts several years after the event. To me, that was the biggest loose end for the entire series.
Other than that, there was the question of the mantis eggs from the end of Season 1 and what happened as a direct result of the destruction of the Suvolte eggs (the potential customers must have been upset, to say the least, and would have been looking for payback from the person who destroyed them),
Whistler: If done properly, W is a good character to have around, someone who can show up in both Buffy and Angel to provide exposition and hints about story direction, as opposed to one time use oracles and "What's that Giles, you say Willow isn't here?" His comic story reveal, where he's a demon x angel hybrid who is working for Twilight, eh?
The Key, the Beast, the Monks and the Knights: Frankly, the mythological underpinnings of season 5 are random and feel like something out of a poorly translated JRPG from the early 90s, or Neon Genesis Evangelion. Especially, for a battle of nameless gods and ancient monks and knights, all this stuff happened in the mid-1970s, when Ben was either conceived or en-souled.
The Summer of '99: What was the immediate aftermath of Graduation? How did they mourn the fallen? When did Cordie and Wes leave? What arrangements were made for Faith? When did Joyce return? How did the State and Federal Government respond when they found out a city was controlled by a Demon Sorcerer and a major supernatural outbreak took place in plain view of many witnesses? Heck, what happened to Sunnydale's Government? And how does this relate to the Soliders who would be seen walking around campus?
What happened to Ethan Rayne after he was busted in "A New Man"? The last we see of him:
By the authority of the U.S. Military, you are being taken into custody pending a determination of your status.
The MPs haul Ethan away.
They'll take Mr. Rayne to a secret detention facility in the Nevada desert. I'm sure he'll be rehabilitated in no time.
I think I'd like to go watch them manhandle him into a vehicle.
If I were Ethan, I would have a contingency plan like a spell that's almost complete and he just has to say the final word of it to get out. That could have been an interesting episode in itself. And of course, he would come back to Sunnydale to get revenge.