The only comparison I can make is between the Axe III and the NDSP Petrucci plugin. There are 3 things I notice in comparing the plugin to the JPIIC in the Axe: (All high gain tones, using headphones)
1) I'm trying to get my string changes to the point where there's no gap, yet there's also no overlap. And I can do it, even in fast riffs, but no matter how deliberate I am in the Axe, there's like a lingering split second of the note (much more prominent on the wound strings) that's almost like it's not letting go, on the Axe. I know it to be so, because I can play the same riff through the plugin, and it's not there. It's a sort of "mud." This is with no effects.
2) There's a fizz in the tones that seems like it's annoyingly separate in the Axe, but seems like it's a true part of the tone in the plugin. It used to drive me nuts in the Axe, so I knew I wasn't crazy in that the very first time I used the plugin, I noticed a difference.
3) This one's harder to describe, more in the context of presets I've tweaked..., the plugin can be harder to "tame." Like, I find myself being reminded much more using the plugin that I have to pay strict attention to any unwanted string noise.
These could be simply because the IR in the plugin is a bit smoother maybe, but this is using the factory presets, but without tweaking the cabs. So it could be that I still need to learn how to dial the tones in better. But it makes me want to use the plugin more often. And I don't think a listener could hear what I'm hearing in a recording, because it's subtle, and the tones are extremely close.
But it seems that these nuances can be what makes us as players, favor one platform over another.