I can't tell you which one is right for you, but I think they're both tremendously great guitars. I've played some recent Prestige Ibanez, and I own a USA Jackson.
Key differences I see:
The Ibanez is a basswood body with a bolt-on neck.
The Jackson is an alder body with a maple through-neck.
The Ibanez is a rosewood fretboard.
The Jackson is an ebony fretboard.
The Ibanez is H-S-H.
The Jackson USA will be an S-S-H or an H-H.
The Ibanez Edge trem has the best action and tuning stability of any trem I've tried.
The Original Floyd Rose on the Jackson SL1 or SL2H is the best-sounding trem I've tried.
The Ibanez neck is very thin and can be great for playing fast.
The Jackson Soloist neck is thicker, more comfortable (for some), and can also be great for playing fast.
Of the higher-end or Prestige RG's I've played, I think they have a more piercing tone than a neck-through Jackson. They sound a little more Strat-like, for those funky, spanky types of sounds.
The Jackson has more crunch, to my ears, and it's great for classic metal. It has tons of sustain and mids. You probably won't mistake it for the sound of a similarly-equipped Les Paul, but it will be closer than the RG.
I guess I like Jacksons more, because of the looks and because not as many people play them. Also, I'm a Yankee, so I feel a bit of a patriotic bond with some of our American guitar makers. But I still love my JEM and my 7-string Japanese RG.