At first, you're strongly attracted to each other -- and this attraction probably blinds you to what are some very basic differences between you. As time goes on and the dust of your romance settles, you start to realize that you are, in fact, quite different, and you have two really different, maybe even opposing moral codes. This doesn't necessarily mean you start arguing all the time; it could occur on a minor level and just lend some irritation to your interactions -- or maybe even some welcome stimulation!
But it could be a lot more serious than that. If you're both feeling as if you're extremely different on a basic level, you probably don't progress as a couple as well as you should. It's natural, if unfortunate, to look at differences as a threat. You might start looking at each other as a stranger rather than your close, intimate friend. You might even wonder from time to time why you're together, which is a valid question to ask. After all, are you looking for a partner in a romantic relationship, or are you looking for someone who serves as a counterpoint to your own personality, someone who holds your interest even as they get under your skin -- over and over again? If you're looking for a true partner, this relationship might not provide what you're seeking. The likelihood is high that you disagree more often than you agree, and that can try even the most patient of souls.