1-2: Introductions.
3-4: Comedy and hints. Episode 4 ends with the revelation about Makoto.
5: Spending time with Makoto.
6: The end of her arc.
7: Mai's arc begins.
8: The school dance.
9: The first half will be a mixture of 13-14. Second half is Sayuri's incident, and of course, Mai's breakdown.
10: Pretty much the same as 15.
11: And this is the same as 16.
12: First half is Yuuichi trying to convince Kaori, and spending time with Shiori. Second half is her birthday party, and disappearance.
13: The same as 19.
14: Their fruitful relationship, er, blossoms. It'd be nice if he and Ayu went to see Mai/Sayuri at this point, just so they aren't completely shoved off.
15: More AyuIchi love.
16: And more, followed by her disappearance. They get three episodes because, you know, this is the main girl we're talking about! Her disappearing is a big thing. It needs to be built up.
17: Yuuichi grieves, as Nayuki does her normal thing of cheering him up. This is like the happy elements of 21.
18: Yuuichi gradually remembers what he did to Nayuki. This would be the more dramatic version of 21, with Akiko's accident at the end.
19: Nayuki lapses into depression, but doesn't do anything. This is where a major change could work quite well: Bring Mai/Sayuri out of hospital at this point, because we already know they're okay. Sayuri's story goes here, and the episode ends with, "Dedette, Yuuichi."
20: Nayuki's scene. Yuuichi remembers what happened to Ayu and runs up to the mountain, and it ends there.
21: Kaori comes over like she did in 23, and talks with Nayuki. She then asks where Yuuichi is, and Shiori, now healed, goes to save him (remember this would of course all happen in the space of a couple of hours). Shiori then fulfills the real Makoto's role here.
22: The first half of the episode builds upon happier times, just like before. Then Ayu returns for her final farewell. After she disappears, the clock scene. Episode ends with Nayuki's apology, at which point she tells Yuuichi where Ayu is. He runs to the hospital and the episode ends.
23: Everybody takes care of Ayu. Yuuichi figures out about the hairband, and attempts to fulfill his promise.
24: The true happy ending. Akiko recovers, Ayu wakes up, everybody's alive and well. We then get her monologues about the seasons and dreaming, followed by the same ending scene we got in episode 24.
This isn't perfect, but I don't see why it wouldn't work. Plus this way, the other girls still play an important role, and don't get shafted.