Well, I think it's more like saying we should prefer temperature data based on tree rings or ice cores (or, even, old mercury thermometers).
"Prefer" is probably the wrong word, so you certainly have a point. "Accept, with a note that the data isn't ideal" is much better. I'm OK with using less-than-ideal data when ideal data isn't available; but I'm disappointed with the number of reports that fail to mention any limitations of their. It's entirely acceptable to say "we don't have enough data to establish whether this claim is true."
Isn't it a bit like saying one should prefer the bible to carbon dating because we've only had carbon dating for the last handful of decades?
It's not that U3 is useless, but one shouldn't assume it properly describes unemployment.