I know that this has been discussed widely in the past, but, in a nutshell:
-First of all, the finish: Aside from the fact that the red paint contains actual samples of Vai's whole blood, the DNA swirl project has yielded what may be some of the finest swirls to date. They range from very subtle wide swirls to extremely complex and intricate micro designs. The color choices are excellent as well. Also, Darren's work does not come cheap
It's not so much a mere finish as it is a work of art.
-The Rarity: at only 300, it's the 2nd rarest JEM out there (at least of those for which production numbers have been released).
Those are the main two reasons. It all really boils down to preferences, opinions and taste. To me the JEM10th, though it is admittedly very pretty, is a bit "plain" for my liking. I'm not a fan of black guitars, therefore the JEM10th is one of the 5 JEM models that I've not owned (along with the RB, PBK, VSK & VSBL) If ya like swirls, you'll like the DNA. If you prefer the understated elegance of a JEM10th, you probably won't like it as much.
Bottom line is: if you don't like the DNA, don't buy one. It's pointless to question the value/price of something like a DNA. A JEM10th is not a DNA, which is not a Crystal Planet. The JEM10th also has a relatively high production number when compared to the DNA & CP. That should be considered as well.
One could also argue that a Ferrari is overpriced compared to a Mustang. They're both cars. One is simply a "better" version of another, right? They both have wheels and get you where you want to go (although the Ferrari just might get you there a bit faster!) Just because the color of one is more attractive to an individual doesn't make it a "better" choice. There are far more factors to be considered than the cost of the materials or the finishes, etc.