My understanding is the Jem neck actually has its own profile (besides having the inlay & top 4 frets scalloped). In fact it is actually a hair fatter than the newest Wizard necks. Personally, the Jem neck is my absolute favorite to play feel-wise. I have newer RG's, and I have played (but do not own) the newest neon re-issue RG's. I have not played a vintage RG 550 in years so I can't directly address that one. As for Jems I own 3, an '89 777VBK, an '02 7VSBL, and a '10 7VWH. Of those, the '89 neck is hands down the best neck I have ever played. However, I really do prefer the newer AANJ neck joint, so the '02 is probably the best compromise between the two styles (it is still a 1-pc quartersawn neck).
So necks aside another consideration is body wood. All the RG's you mentioned are basswood, whereas Jems are available in basswood or Alder, depending on the year & model. If you have a preference between tone woods this could be a decision maker in and if itself.
Additionally, you are of course looking at different pups/electronics between the RG & Jem models. Jems of course sport the DiMarzio EVO sets, and RG's generally have "DiMarzio designed" Ibanez pups. This, in my opinion, should be the lowest consideration on your list. Pups are so easy and relatively inexpensive (compared to the cost of the guitar) to change out that it really isn't a big deal if you love the pups a given guitar comes with. I would worry more about the "feel" being right for you. That's hard to change much. If you find a guitar that feels great in your hands there is a ton of stuff you can do to dial in the tone you want (pups, caps, pots, brass/titanium tone blocks, etc).
Finally, you may be looking at different tremolo setups (Edge, Edge Pro, Edge Lo pro, Edge III, Edge ZR, etc). Some people have very strong preferences in this department so make sure you're happy with the trem before you buy. Play them a lot! Palm mute, dive bomb, trill, pull up, light vibrato, etc. so you have a good feeling of a particular trem's action. While you may be able to change out the trem later, it can sometimes be a complicated procedure depending on whow different the dimensions are between what you got & what you want. You may have to re-rout the body or pull the studs & plug & re-drill for new studs (although, I think the stud spacing is pretty similar amongst the Edge lineup... But I'm not sure so def find out if you have a preference!).
Anyway the point is there are differences and to some these differences are small while to others they are huge. Ultimately only you can decide how significant they are to YOU.