It really depends what you want...
They are about as opposite as you can get.
The VWH is very nice (I'd like one eventually) but it's mostly flash that you are paying for imo. The inlays, the gold hardware etc. It's got a wonderful neck and the stock pickups aren't horrible (although I'd gut'em for sure). Overall a really nice guitar that's tough to fault. But when you think about what you get for what you are paying, the JPM is a better deal imo.
If you do like Kirk said and scrap the inlays/sig finish, you can pick up a loaded 6 string JPM for under $1500 I'm pretty sure. It's not as flashy now, it's a much more reserved guitar (which I like since I'm not flashy either
), but it's far more versitile based on the pickup/piezo setup alone. Personally I prefer the EB neck to the JEM neck, but that is me. I think the finish and fretwork of the EB is far superior however, but I'm sure I'll get flamed for that.
I think what it boils down to is what do you want the most? Style/flash or versatility/value?
If it's style/flash, get the JEM, if it's versatility/value get the JPM (and a little exclusivity as well, JEM's are a dime a dozen, especially VWH's