Based on my experience, all skills count toward the cap, although I also think that the weight is not linear: for example, any skill increasing from pitiful to awful will have a negligible impact on capping compared to any other skill popping from marvelous to prodigious.
So, for example, based on the fact that centers typically have, say, very low outside defense and very high rebounding skills, they will veeeeeery likely tend to reach their cap due to RB rather than OD. Still, if you have a C with prodigious OD, that will count versus capping as much as a prodigious RB.
But don't take my word on it, after all these are very extreme cases therefore they're hard to evaluate.