It's About Values, Not Issues
I think the issue here is really values and not "issues." I've heard of many couples whose political votes would cancel each other out as one voted for Bush and the other Gore, for example.
Yet, the thing that concerns me about your situation is that the differences may be more than about voting for particular candidates, but may reflect an inherent difference in values.
I would worry if you guys differed around fundamental issues like the place of women in society (working or stay at home) or if you had very different views on how children should be raised.
Decide What You Can Tolerate
Any difference in a relationship can be uncomfortable; yet, the differences need not break you up. You have decide what's offensive and what's tolerable.
I think it's possible to bridge your differences if your core views of what matters in the world are complementary.