Look at Kirei a bit. Fate route, he's like a pretty shitty, forgettable priest. He's irrelevant in UBW to the point where he's unceremoniously killed off because someone else in that route can already criticize Shirou's ideals (and thus be the villain of the route. protip: it's Shirou's own ideal, aka the redman, aka communism) so much better than he can. If you look at him in HF, he's...a strangely reliable ally and helps out a decent amount? And then comes back near the end to pose as the final challenge for Shirou to overcome. Also he's fucking adorable with the mapo tofu shit. What I'm trying to say though, is that at least to me it feels like Kirei is kinda just thrown into HF (and manages to be the best part of the route anyway). He doesn't have any stake in the conflict of sisters or Zouken's bs, he just cares about birthing the thing inside the grail. He (specifically, the plotline of him wanting to protect the evil being birthed by the Grail) could probably be taken out of HF, and both HF and his part of the plot thrown into a different route altogether would still work at least on a thematic level. So what would happen if Kirei appears in a final, Illya route instead?
It goes back to the idea of bridging the gap between HF and Fate together I brought up earlier, like with Saber possibly serving as Shirou's servant again. Kirei could come back as the main villain again but this time he'd be used so much better than in Fate, and we know this because we've already seen it happen in HF. The contrast between his first appearance as a villain and here is the attempt to bridge HF and Fate, and also a nice callback to when you began reading this VN 50+ hours ago. The only problem I could see with this is that, if memory serves, Sakura being the Shadow actually does relate to the Grail giving birth to the evil being inside it. If I remember wrong, hurray, but if I didn't, that'd be a plot detail that'd have to be resolved somehow. But on a thematic level I think it fits. Something about poetic justice and pattern recognition iunno
Here I'd also like to suggest another possible story element of what Illya's route could've been. Shirou in this route would be closer to his Fate self in term of power level. Why? I actually love the power escalation from Fate to UBW to HF, but where else can you go after HF? Make Shirou as strong as his HF self without the limitations? For what thematic purpose would that have? His HF self having about as much firepower as a servant is because that's the route where he directly takes the mantle(technically, shroud) of being a hero to fight a tangible threat. He needed to be a hero who could fight so he can actually face the dilemma of deciding whether to kill Sakura or fight the rest of the world for her. That's not actually as important in his fistfight with Kirei, because by then he's resolved to kill the thing inside the grail before it could be born. That's a decision he could make as just Emiya Shirou and not an Ally of Justice/Superhero/whatever translation people go with 正義の味方 these days. Actually no, it'd be a decision he makes because he's a 正義の味方, but it wouldn't need him to fill the role of a classical hero that he does in HF, or is saying that just sophistry? I don't know either. Back to the point, Shirou being weak again is well, yet another attempt to bridge HF and Fate Shirou together in a more literal way, but it'd also work as a substitute to the original fistfight. In the final product of HF we did get, it was a fistfight because Shirou pretty much exhausted everything and he's getting torn up inside and could only punch and kick. If he was just a normal human in the first place, weaker than his UBW self, you'd achieve a similar effect, especially if he's injured beforehand. He'd still only be kicking and punching. You'd lose out on the vivid descriptiosn of his body slowly turning into swords but that's a fair trade-off, maybe. In return, Illya route Shirou would be a return to form, back to the original, weak master protagonist we began with, without any empowerment from Archer. When he jumps into that fistfight with Kirei, regardless of the actual hypothetical context, it'd be just him going into that scene. Not the Emiya Shirou who already activated the fuse known as GARcher's arm and was going to die anyway, but the Emiya Shirou who's a dumb uneducated mage and practically just a powerless teenage boy. It'd be that Shirou doing fisticuffs with Kirei, with the life of the evil being in the grail and the rest of the world at stake.