all im saying is that emg's are designed to make up for lack of tone wood thus them being active because they need that extra punch from somewhere other then the wood and ibanez are great tone wood guitars and putting emg's in them i think robs you of what you have. i dunno if someone can set me straight i woudl love it but thats how i see it and i have owned many many guitars with emg's take a guitar with ok pickups and replace them with emg's and you have a great metal guitar, scooped badass metal, play clean tho and you got another story. they are good for what they do thats all. not very versitile....i own emg's i love them but they are very very linear.
They do impart their own freqencies on the guitar a little bit by being active, but at the end of the day the signal being put through that little preamp is still the signal generated by that string on that bridge and that piece of wood. The differences between two emg equipped guitars are pretty obvious as long as the guitars in question are aswell. They're far from a 'compensator'.
In terms of construction, jackson necks really aren't built all that different from ibanez. Thin and flat, low action. In theory they should sound even better because they still use a block heel, but I'm doubtful thats ever made a true difference myself, I like the AANJ just fine.
Oh, and I'll point out that the Reb Beach Koa signature actually came with EMG's as standard on the more expensive model, and Ibanez own pickups on the lower end models, and both sound fantastic.
It really is just an option. Its a different style of pickup and has its advantages and its drawbacks, but frankly I think writing them off as some kind of 'lame tonewood cure-all' isn't just presumptuous but about as close to 'wrong' as I would dare to label someone elses opinion.
Double edit: Oh, and the 'reason' for them being active isn't the one you've assumed either. Active pickups can generate a much louder volume with a much lower output magnet, so they can achieve a pleasing sound with much less string pull, so you can set them much closer to the strings with no problems, AND high output when needed. It also means they can make high output humbuckers that are very bright naturally, as traditional passive humbuckers become much much darker in tone the more coils you add to the windings. There are ways around it, but none of them completely alleviate the 'higher output = darker tone' problem you'll find in passive designs.
Different approach to solving some of the problems in passive pickup design.
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