Honda-san would be a more stabilizing influence for Miyuki. He's older, more mature and more mellow. However, he's not exactly an exciting sort of person. I think even Miyuki would prefer someone more unpredictable.
Nakajima's affection for Miyuki is very steadfast and very admirable. He deserves Miyuki more than anyone else. I believe the feelings between the two of them are reciprocatory, so they should be together for as long as they still care about each other.