John is in love with Mercy.  As he tells Kit, "It has always been Mercy, from the very beginning".  John loves Mercy just for being the serene, loving, selfless person she is; he is aware that there are many things she cannot do because of her physical limitations, but when Kit points this out, he says,

"Then I will do them for her...I don't want a wife to wait on me...for Mercy just to be what she is..I could never do enough to make up for it".

John and Mercy are perfectly suited for each other.  Both are gentle, deeply spiritual souls.  John is training to be a minister, and Mercy is almost otherworldly in her devotion to the true tenets of Christian faith.

When John comes to the Wood house with the intention of asking permission to court Mercy, however, Judith's impetuous outspokenness changes everything.  Judith has set her sights on John Holbrook herself, and when John comes and intimates that he wishes to speak to their father, Judith immediately jumps to the conclusion that he has come to court her and not Mercy.  With "irrisistible...radiance", she takes things into her own hands, essentially speaking for John to her father.  John is "dumbfounded", but "such utter happiness and trust (shines) from (Judith's) blue eyes" at the thought that John loves her, that John falters when he tries to explain his true intentions, and he says nothing.  In "(the) moment of (his) hesitation, he (is) lost", and he ends up in the awkward situation of courting Judith instead of Mercy (Chapter 13).