I would say that beating Vegnagun (and the Tidus "clone") in FFX-2 symbolizes Yuna getting over Tidus's death. Vegnagun was like the demon in her mind left by him dying. Such that, when you defeat him, it's your choice to save Tidus or not save him-- she's already over it
In a way, that makes the FFX-2 boss(es) one of the best. Fighting Sephiroth, Zeromus-- they don't symbolize much!