Many of my favourite couples aren't canon couples, actually, but I think that they should have been!
1. Yankumi/Sawada Shin (Gokusen 1), canon in the original, but not in the drama
2. Sae/Kai (Orange Days), canon
3. Momo/Sumire (Kimi wa petto), canon
4. Sakura/Hiroto (Last Cinderella), canon
5. Akiyama Shinichi/Kanzaki Nao (Liar Game), non-canon
6. Mazuru (Son Neion)/Choukun (Tempest), non-canon but with better chemistry than the canon couple
7. Tanizaki Rei/Kiyama Ryuichiro (Iki mo dekinai natsu), depends on how you look at it...
8. Koga Ikumi/Machida Hina (Koukou Kyoushi 2003), canon
9. Nagumo Jun/Segawa Rio (Control), non-canon couple with potential!
10. Rui/Tsukushi (HYD) ...sorry, can't help it, that's the way I feel!