I'm not really saying that I like the 550 better than a JEM, the JEMs get better quality control, come with nicer pickups and, on the VWH and VSBL, alder bodies instead of basswood. The hardware is comparable on both, in fact, it's the same on the new JEMs and the Prestige 1550 and 1570s. My 550 has the original Edge, works fine for me, I don't get hung up on the regular vs Lo-Pro thing, they both work. Neither does Vai apparently, Evo tends to sport a regular Edge most of the time now.
The biggest difference in the guitars is the feel, the Wizard neck on the RGs is thinner than the JEM neck, except for the DBK (and some older models, i.e. PBK) which is very close to the Wizard neck. I personally like the JEM necks better, but I can get used to about anything. The RGs have jumbo frets while the JEMs have 6105 fretwire, the 6105 is about as tall as jumbos (6100) but thinner, I like the jumbos better. In the past the JEMs supposedly got more attention to detail, but now that the 1550s and 1570s are also Prestige series, that can be argued. If you buy a 550, 570, 1550, or 1570, you will probably end up replacing the pickups, the Ibz pickups are good, but not great.
Are the JEMs better than 550s, probably yes, but not insurmountably, the RGs came from the work with Vai on the JEMs. Are the JEMs worth "that" much more, again, it's a totally subjective question. The JEM is slightly more expensive to build, and the pickups cost more, although I'm sure Ibanez buys enough from DiMarzio to get a substantial discount. Do you like Vai? Alot of the money from the purchase of a JEM goes to his pocket, I'm sure he has a pretty sweet deal and gets quite a bit off the sale of JEMs, more than Joe I would suspect, just from comparing the prices of the JS
's vs JEM's. I like Vai, I own all of his music and have played many JEMs so I don't mind him getting some of my money. I tend to stay away from the models that he is most associated with because I would rather "be me". By the same token, I have owned a slightly beat up VWH, it was a killer guitar.
For now, the 550 is the guitar for me. I may pick up a JEM again at some point, maybe a DBK if I can get rid of those gawdawful screw head inlays. The VSBL is a very sweet guitar, and if you haven't seen one up close, the color is very nice and they play incredible. I like basic black, the 550 is rocking my world right now.
I guess the point of this rant is, if it's worth the difference between the 2 for the Vai-ness of the JEM, go for it, it's a great guitar. If it's not, get the 550, you'll love it, it's also a great guitar. Try one first though, the neck is going to be alot thinner than the Fenders you've been playing and you may or may not like it.
BTW, the first new (not used) guitar I ever bought for myself was an '87 or '88 black 550 with a rosewood fretboard, because I couldn't afford a JEM at the time.