Epi Boneyard comes out of Korea, right? Curious that no one has actually mentioned the major reason for the difference in price - The Gibson is made in the USA, by people who get paid US style salaries, the Epis are made in Korea, on Korean salaries. Nitrocellulose lacquer DOES make a huge difference to how a guitar "breathes" - if you compare a Custom Shop '58 to, say, a Les Paul Classic, they sound and feel totally different - the only similarity is the shape! Gibson Custom Shop guitars are actually hand made - no sh*t! (by people using machines though, not whittling them out with a penknife)- that leads to each instrument being a little different from its mates, and, as some people have noted, rather varying quality control (though I've picked up maybe a hundred Gibbo CS instruments, and only one of them, a black 335, genuinely sucked) - are they worth the money? Is a real '59 Les Paul worth $100K? - it is if that's exactly what you want and you've got the Pesos to get it! I gigged with a CS 57 for a few years - great guitar, too heavy, and it refused to stay in tune - so Gibson sure got the guitar historically accurate!
If you can afford it, get the Gibson, but try to find a second hand one - let someone else take the depreciation pain!