It's not really fair to say, "Yes but without his best surface he sucks." If you do that, why bother comparing? Take out the best surface from Federer, Djokovic, etc and how do they stand?
see, the thing is, so many of his matches against the top 4 are played on clay because the rest of the top 4 (barring perhaps murray) can consistently get to the SF and F of clay events, whereas nadal is not nearly as consistent in getting to the SF and F of non-clay events compared to fed and djoko.
so in way the rest of the top 4 are punished rather than rewarded for their consistency on all surfaces by reaching late rounds at clay events where they continually lose to nadal, but nadal hardly gets to lose in the late rounds at non-clay events because he isn't good enough to get there consistently in the first place. this is also why the fed-nadal H2H is pointless, off clay nadal has a losing record against fed (although only slightly)