Based on my (admittedly limited) experience, one relationship-breaker is a failure to model each other's minds correctly, and, similarly, interpreting identical data in very different ways, which leads to serious communication problems. Also, along these lines is trust; it tends to be harder to trust someone if you can't predict their reaction or you expect they may react with (what you percieve as) totally disproportional emotion to a minor (as you see it) event.

Rationalists should, in theory, be somewhat better at avoiding these pitfalls, both because they think in similar ways and because they're rationalists and thus have a shared language to address these problems and some consciousness that they exist.

This may offer some explanation of why rationalists might prefer rationalist romantic partners, since it (may) increase the odds of effective communication and minimize both the frequency and magnitude of misunderstandings.

The following comments are evidence that female rationality is important to at least some male rationalists. Note that the first comment was upvoted by 7 readers.

I know I would love to have my next girlfriend be a rationalist (if only to avoid my most recent failure mode)

http://lesswrong.com/lw/ap/of_gender_and_rationality/7me by MBlume

But she loves magical thinking, she is somewhat averse to expected-utility calculations, my atheism, etc. . . . We love each other but are scared that our differences may be too great.

http://lesswrong.com/lw/zj/open_thread_june_2009/rxy