I've always imagined a Fate/Stay Night sequel to be a continuation of a particular route, with the existing cast of characters along with some new faces. This does, of course, entail the central problem with writing sequels to a work consisting of discrete, parallel narratives or "story arcs" - either you pick a canon ending, or you just end up with some nebulous, non-canon "dream sequence"-type thing that's more fan service
than an actual narrative, a la Kagetsu Tohya and Fate Hollow Ataraxia.
Regardless, assuming that what I've heard is reliable, and the Heavens Feel True Ending is, in fact, the true ending:
Center the story once again on Fuyuki, around Shirou's life and Sakura's newfound duties as Magus Protector (or whatever the official name for Rin's position was) of the city. Suppose a heretofore unheard of magus is on the loose, sucking people dry of mana and killing them, turning them into zombies, or doing something sufficiently evil. Sakura, Shirou, and Rider begin patrolling the streets at night to stop him. When they eventually do encounter him/her, they expect it to be an easy fight. In addition to Sakura and Shirou's abilities, they have what should be the only Servant left in the world - one with high magic resistance at that.
But *gasp* - it turns out she's not the only one left! Somehow, our enemy Magus has done what should be impossible given the destruction of the Grail, and apparently summoned and formed a contract with a Servant. Perhaps the Servant is stronger than Rider. Or perhaps it's weaker, a hero that would ordinarily fall before a full-strength Medusa. Our new magus, however, makes up for the difference somehow - perhaps he/she has some trick up the sleeve, wields some unorthodox magic thus far unexplored in Nasuverse e.g. voodoo or onmyoudo, or simply has a group of henchmen armed with semiautomatics. Perhaps a combination of all three. In any case, it seems our cunning new villain has been expecting our three protagonists, who are quickly overwhelmed and forced into a hasty retreat, barely escaping with their lives - but not before the enemy magus has a chance to taunt them.
For some reason, this sinister magus knows what went down in Heavens Feel. He/she knows that Sakura once had a contract with Angra Mainyu and under its influence murdered hundreds of people. He/she knows that Shirou, deciding to protect the one he loved above all else, allowed these people to die, when he could have prevented it. He/she decides to pull a "not so different"
speech, along the lines of "what right do you, you who sacrificed others for your own happiness, have to judge me?" he/she says. Depending on the personality of the villain, he/she may attempt to "twist the knife", aggravate old wounds, pick at their insecurities, etc. Shirou and Sakura along with Rider are forced to flee, injured and demoralized. While they recover, our new villain is free to do as he/she pleases, and the story goes from there. Other new characters show up, existing characters return, meanwhile our three "heroes" must figure out what the villain's plans are, why he/she's killing/hurting people, how he/she managed to summon a Servant, and most importantly, how to stop them, all while battling their own inner demons, or something like that.