Zoe and Wash touched a lot of hearts because of the transposed gender roles they represented and the general odd couple feel to their relationship. And then it was basically the same thing with Simon and Kaylee; city mouse falls for country mouse. Mal and Inara were a classic mismatch, too.
None of them are totally ineffective, but it's a little too clear that they were paired up that way because they're mismatched, and not because of their chemistry. They all have traits that the other can admire, but there's no particular reason that they'd find enough common ground to choose each other.
If you met the characters individually without the context of the plot, the obvious matches are Mal/Zoe, Wash/Kaylee, and Simon/Inara. Thing is, I think they're obvious because that's how it would happen in real life. People tend to fall for each other when they share a history or similar interests or a certain level of education.
Not a big deal; I still like watching their relationships and I didn't need a ship anyway. Just makes me think about what makes a romance romantic.