Well, I'm no expert on the exact value of older JS
models, but I really don't think that's the main issue here anyway. The fact that you're even considering a trade indicates to me that you're not getting rid of the guitar because you need money. I have to assume then that you don't like it, or at least would prefer something different. If you like the RG550 more, then this trade probably makes sense for you, whether or not it makes sense to anyone else.
In terms of actual market value, I would have to think the two guitars aren't that far apart, but that depends on their condition of course. Comparing their ages, the RG is practically new, though that doesn't necessarily mean it's in better shape. Assuming they are both in excellent or better shape, I would expect that the JS1 would fetch a little more than the RG, at least if you find someone that really wants a JS1, which you seem to have.
Of course, no one else can tell you which guitar you like better, which will probably be the biggest factor here. If you're concerned about making a bad deal in terms of future value, I wouldn't be. Neither guitar is ever likely to be worth considerably more than it is today, both have a degree of collectible potential, but nothing Earth-shattering.