At first, Ahiru and Fakir didn't like each other at all. As the story progresses, their friendship is growing and Fakir also began to have feelings for Ahiru. Fakir became protective and concerned for Ahiru, When he found out that Ahiru was actually Princess Tutu and was really a duck, he was shocked and embarassed that he cried infront of Ahiru. Fakir also confessed to Ahiru that he will always be with her.
Also, the song playing during their pas de deux in ep 25 is The Last Farewell from Prokofiev's Romeo and Juliet; which was the last time Romeo and Juliet saw eachother alive.
And even though it would seem that they fell deeply in love with one another, their relationship never moved past friendship before the end.