biggest differences I can think of are lock nut vs non locking, fixed vs floating vs vintage trems.. and string gauge of course

Another factor that I didn't see mentioned yet is how old the guitar is. In other words: Does the JEM have more mileage on it than the RG? I own several RGs dating back to 1993 and all things being equal, the older guitars are typically "easier" to play than say my brand new RG2550. The springs are more "broken in" and the frets have considerably more wear. They therefore require a bit less effort when bending.

Having said this, I don't think there is any one definitive factor here. There are probably dozens. Many of which have been mentioned above. Still, I've played identical guitars out of the box and had one feel "stiffer" than the other. Go figure.

Interestingly, in the March issue of Guitar World, this very question is raised Matt Bruck's "Tech Education" column. His answer in a nutshell is: he really doesn't know. LOL

Have you checked the truss rod adjustment on the RG?

Is your trem perfectly balanced? Why can't you get the action as low as your JEM? I recently set up two rgs (one was a 2550). Out of the box the string tension was very different but after setup, almost identical. If the neck bow is different, or the trem tensions are not set right, it will be hard to get the action as low as possible. Make sure the knife edge on your bridge is parallel to the guitar body. (This will be a lot easier if you lock the bridge in the correct position, retune, set action, intonation, then remove the block and fine tune while alternating between tuning and slight spring adjustments).

As mentioned in other posts above, the major factors are scale and string gauge. Since both guitars are the same scale and have the same string gauges you should be able to get the tension pretty much the same, aside from very minor factors such as neck shape / leverage, frets, etc..

Sorry for stating the obvious here but remember that string tension, along with string length and gauge, are how you arrive at the note you want. So with any given string gauge and length/intontation, any change you make to the tension will also change the fundamental note. So the thing about the tuner screw adjustment was silly because even if it worked it would have the same affect as just turning the tuner (which also increases the string tension - duh).

Even though the guitars are the same scale, if the intonation (saddles) are adjusted at different extremes the tensions required to achieve the same note may be noticably different. If this is the case be sure to check the truss rod / neck bow and trem balance, and if you change them, then re-intonate and reset the action and retune.

IF ALL ELSE FAILS... just get lighter gauge strings.

even on parts of the neck where action difference is not noticable, the action difference will change the tension slightly, same as having a SLIGHTLY longer scale on the guitar with higher action because the string is in fact a little longer from breaking point to breaking point.