Re: AANJ or square heel
It's just personal preference, really. The AANJ was designed in the first place to be a "better" bolt-on system in that the heal of the guitar doesn't get in the way quite as much as a standard block heal. Many people (I might even say most) seem to prefer this newer design, but there are some who prefer the old-style heal. I know Paul Gilbert claims to prefer the block heal for tone, but really, the differences in tone are only going to be detectable to someone with very good ears, and even then, it's personal preference that decides which is "better".
As far as the reissues, I suppose Ibanez was just trying to make them as much like the originals as possible. Then again, they did include the newer 5-piece Prestige neck design, so who knows. In the end, unless you're playing on the 24th fret a lot, you probably won't notice any difference in playability between the two designs.