Prophecy is nowhere as good as fs2
As far as the series go, it depends a bit of how you look at it i think.
Gameplaywise Freespace 2 especially beats any of the Wing Commander fair and square in my eyes.
But Wing Commander, especially 3 and 4 are still the undisputed kings of "presentation" with their huge amount of video sequences featuring real actors.
They also "feel" quite different... Wing Commander mostly being a "classic" space-opera where the good guys always win in the end, while Freespace 1/2 were quite a bit darker and mysterious.
But i don't really think it matters that much which game is "better"... it's not that easy to give a definite answer with either game having it's strenghts in quite different areas either... and for any fan of the genre it's propably a crime to miss any of the Freespace, Wing-Commander, X-Wing/Tie-Fighter and even I-War games anyways.

As far as Prophecy specifically goes however, i would be inclined to agree, while it's still sort of a "must" for fans of the genre, it outright sucked once you compare it to either the previous Wing Commanders or to the Freespace series lol.