NJ/NY Tax implication?

I am married and live in NJ. I worked in NJ and my wife worked in NY in 2008. When I fill out Schedule A for the NY jurisdiction, it seems to me that my income should not be factored into line 2 because that drives down the credit percentage. It should only compare my wife's NY and NJ income, not her NY income and both of our NJ income. If it only compared her NJ and NY income, that would be apples to apples. It doesn't seem fair. Is my thinking flawed? My federal return is filed jointly so I have to file the NJ return jointly. Can somebody shed some light on this for me because it is real confusing. Thanks!