Issues with the Linnean System - Alligators, oysters, and "familyness"

How are alligators like oysters? - Both the groups Alligatoridae, including modern alligators and caimans, and Ostreidae, containing modern oysters, have the rank of "family" in the Linnean system, suggesting that they are somehow biologically equivalent. Many measures of equivalence can be imagined.

But alas...

So what, exactly, does it mean to say that oysters and alligators are related at the "family" level? Can it be that establishing taxonomic rank is, "more of an art than a science," involving the interpolation of new groups into the preexisting system?

That's OK if you only intend to use the system for information retrieval, but academics who attempt to measure patterns of evolution by counting, say, families inevitably must confront the fact that they really are not counting equivalent units. Stephen Jay Gould famously fell for this in his book Wonderful Life.