Evidence shown in the series that Aya and Junpei are destine in some sort of fairy tale way, but they wouldn't have match well. Both were too dependent on each other, conversation are base on novels/movies, and deep understanding for each other was baseless.
Nishino took the extra step to understand Junpei deeper feeling, supporting him, and give him broader perspective in life (yes, would benefit his skills compared to introvert girl).
All the evidences of fate etc.. was indeed in Aya corner, but Junpei/Nishino created their own destiny and walk on (there is evidences of this as well, remember the 1408 paper? Junpei rip it apart and he corrected Nishino and said he loved only her).