OK, I think I see what you mean. What I meant is that jou is the object case, and in English it is often marked by adding to. However, there are clearly cases where this is not the case. Here are two examples where the same English sentence requires one or the other translation, due to different contexts.
Wie houdt van ijs? - Alleen jij. (Who likes icecream? - Only you.)
Wie heb je lief? - Alleen jou. (Who[m] do you love? - Only you.)
Note that in English the object case of who is traditionally whom, though using who for the object case has long been acceptable.
First, there is the same problem as with alleen je: In this position and with nothing else around, it's almost certain that the jij in alleen jij is stressed and therefore can't be shortened to je.
Another issue is that even the phrase alleen jij appears to be relatively rare outside the frequent idiom alleen jij en ik. I guess this can give us an idea about slightly different shades of meaning of enkel vs. alleen. Similar phenomena exist in English, where for some uses only is better and for others just is better. ("Only you would do such a thing." "Just you and me, isn't that great?" - Swap only and just, and the two sentences will sound slightly off.)
Alleen sometimes acts as a false friend for speakers of English and German because in Dutch it has the meaning only in addition to alone. As the example only you vs. you alone shows, there is an overlap of meaning anyway. I guess in Dutch the disambiguation, if needed, is often achieved via word order.