I suggest to dig in this forum a bit. There have been a lot of such threads before so I bet you'll find your answer. But in general...yeah wood has been changed so that's a serious difference, body is slightly bigger and without hand scope plus it has some more cutway space - so the access to higher frets is more comfortable...anyway I'd check this great forum for answers first.
alrite fella.if you can afford it go with the BFR as its worth the extra money.different wood makes it abit heavier but the sound more than makes up for it.the neck is finished also compared to the unfinished neck on the standard but i dont think it makes ahuge difference.check out mine which i got over amonth ago now. http://www.ernieball.com/forums/music-man-guitars/28463-i-hate-musicman-guitars.html