Buffy/Willow: I think this is the most impossible pairing so far. Makes Riley/Giles look like a snap in comparison. I could see a little Buffy/Faith arc late in the series, but the most likely scenario with Willow seems like an unrequited pash. But if you keep Xander as is, you'd find yourself in a situation where Buffy's two best friends *both* have crushes on her, and that's just...icky.
So, going for the impossible scenario. Season three, Oz graduates and leaves. Willow takes it to heart, believing he didn't stick around because of her betrayal with Xander. She's mopey and she's also more vocally frustrated by her lack of magical progress. Play that up earlier as an arc for her; Giles at first thwarts her, but Willow persists and he finally unbends and sets her to a course of study designed to keep her on the right track, so that she's not going off unsupervised and playing around with forces she doesn't yet understand. She complains to Buffy once or twice that he's deliberately hobbling her, keeping her pace slow. Early in senior year, we meet Tara, a transfer student. Tara has a few friendly class-related exchanges with Willow, and then of course some big monster-plot of the week occurs and Tara discovers the evil underbelly of Sunnydale while at the same time the Scooby gang discovers she's a witch. This might be an AU without Amy.
Tara bonds with Willow and introduces her to a different world of witchcraft, one that seems exciting and free of Giles's "patriarchal" constraints. Tara comes from a long line of witches (her late mother was one) so she's knowledgeable and has common sense, and after getting to know her Giles isn't so much worried about her influence on Willow. Willow, initially enthused, soon starts to feel frustrated and held back by Tara as much as Giles. All of this is background to the big Buffy-Angel-Faith arc and carries over into season four. In romantic terms, Willow and Tara's friendship, just as in standard canon, gradually turns into romance, probably late in senior year. They make cute girlfriends, and Willow gets a bit political as she goes through her coming out process.
Season four, Xander hooks up with Anya, while Willow and Tara take a room together, and Buffy suddenly finds herself feeling strangely rudderless and solitary. Her friends have relationships and are doing their own things, and she keeps bouncing between them and then feeling like a third wheel. She does some light college-boy dating but seems to keep driving guys away--she's sabotaging herself. It should be obvious and played for humor for a while. During this time, we also start to see signs that Buffy is jealous of Tara. She feels displaced and at first it seems like an issue of friendship. Buffy's our heroine; she wouldn't be *romantically* jealous, right? Tara is ultra nice, though, and so Buffy's kittenish attempts at pique keep fizzling out damply, leaving her vaguely sighful and smiling as she resumes being nice to Tara in return. And we can't fault either of them.
But meanwhile Willow has been escalating with the magic and in the middle of the season, she talks Tara into trying an experimental spell against their current demon nemesis. The spell goes wrong, something tragic happens to Tara; she's possessed by a dark spirit, a la Darth Willow, and allies with their enemy. Willow is torn up and blames herself. It's not *entirely* her fault, she had good intentions, and Buffy tries to assure her of this while Giles simmers more ambiguously. They save Tara after an ep or two, dispossessing her; but on returning to normal she's stricken by the things she's done. She lies in bed, face turned away from Willow, tearful and unresponsive. Willow offers comfort, but it's much like her attempts at reassurance in early season six--we're dubious that she's going to scale back or give up on magic, and Tara doesn't seem convinced either. She's sad and hurt and the audience can see that she blames Willow for what happened, at least in part, and that it's put a deep rift in the relationship. She tells Willow that there's a deep power in her and that it scares her, because she isn't sure Willow can control it. The next episode we learn with shock that Tara is leaving. She's packed her stuff, everything's boxed up (a la Oz's departure) and Willow is bereft, pleading with her to stay, but Tara can't.
After she leaves, Willow tries hard to leash herself and manage her magic. We get some interesting Buffy/Willow parallels--at the same time that Willow is struggling to regulate her powers, Buffy is stretching into hers in new ways. Giles advises Willow to discipline but seems to be encouraging Buffy to blossom. Really he's only doing what each of them needs, but Willow feels it's rather unfair. Willow comes around to thinking that the best way to prove she's useful is to help Buffy with her slayer mojo. She wants to try things that Giles doesn't know about. Buffy's unsure, but Willow talks her into it, saying she's learned from what happened with Tara, she won't make those mistakes again. They patrol together and do some kick-ass work, combining their powers to scour Sunnydale of demons on an increasingly wider scale. They're juiced on the effects, and Buffy mentions how she used to feel sort of like this with Faith, except this is the good kind of rush she assures Willow, and Willow confesses how she used to be jealous of their slayer bond, and then *Buffy* confesses how she used to be jealous of Tara. And they're all flushed and jazzed up, but also shy and girlish as we start to realize how flirty everything has gotten between them.
And Buffy has probably had some bad boyfriend experience recently that makes her say, "Men. Who needs them." And Willow sunnily agrees with this philosophy, which makes Buffy giggle. And then they share a sudden, tentative, giddy kiss and Buffy's all, "I'm not sure." And Willow's like, "It's okay. We can take it slow." And they become closer in their new special friend way, and at some point the others figure out that they're being all cuddly on Giles's couch for a reason other than conserving body heat, and Xander boggles and perhaps goggles, and Giles seems disturbed. Later he talks to Buffy and tells her that it's not his place to interfere, but--but she won't hear what he's going to say, cuts him off. Angel comes to visit and he and Giles have a talk, and we learn that Giles is not sanguine about the relationship because he considers it risky for a witch to have influence on a slayer; historically, there have been Incidents. Angel is still boggling with an almost Xandery boggle at the news. "Buffy and Willow? And you've...seen this? I mean, you're sure." Giles, dryly: "Do you want video?" Angel: "There's video?" Giles, sighing: "Please focus."
And...I don't know. Something mojo heavy happens toward the end of the season and it freaks Buffy out and she breaks things off and confesses that she really just wanted to be closer to Willow, to be friends again like in high school, and Willow is upset, saying that Buffy can't just play with her feelings, and there's a rift, but they mend it and resume a sweet, sexless friendship, and the Initiative explodes, raining demon bits across Sunnydale for miles and miles, and as the gang stands in wonder on the gore-splattered ground, a rainbow rises across the sky and they all smile and sing a happy song.
Thus ends Buffy's year of college experimentation and friendly lesbianism.