Could indicates the possibility, the potential. Would does not carry any potential. It carried a notion of choice. In this context, would could indicate disappointment, or even slight reproach (but not necessarily, it depends on the tone and rest of the context): You could have come but you didn't, you chose not to come.

The could sentence simply indicates that "you" were not able to come with "me" (and I would have liked for you to come with me).

Hi Kevin,

Just a note for your interest: 'I wish you would have come' is mainly used in U.S. English. The standard form for British English is 'I wish you had come'.

     VERY CLEAR-CUT DIFFERENCE. THNX