I tend to look at the RG as the lower cost JEM. They're basically the same, and as the original poster pointed out, the RG was designed to be a lower-cost option while still retaining a lot of the look of the JEM series.
Personally, I'd take an RG over a JEM simply because I like to mod 'em my way. I'm probably replacing the pickups in whatever I buy, so that cost is added to either guitar. I like bound necks. I save on the base model, then apply the difference to make the guitar look and feel the way *I* want it to - not Steve Vai. I don't buy signature guitars because they are someone else's idea of a great guitar, not necessarily mine.
I still haven't found a JEM that could kick my RG1200's ass in the price range. The VWH is close, but cost - plus the fact that it has no binding - puts it out of the RG's league.
Some people look at it like - "Hey, the JEM has less wood due to the routings, I'm getting ripped!"
This is my opinion, and it's like ice cream - there're 31 flavors for a reason.