Was thinking about this for the new petrucci plugin that came out.
I just put some up on the Rig Exchange. Search "MAB ArkPet".
I agree with the OP that I much prefer the tones inside the Kemper, although the plugin presets did have some good effects settings that matched particular song's sounds. Most of the profiles I did, however, were basic rhythm sounds and a handful of lead sounds - I just threw my normal effects on there.
I prefer them Kemperized mostly because exactly like OP said - the gate is really screwy, the "double tracker" sounds like garbage, and the core tone is rather noisy. Similar experience - noise went away in profiles to a large degree, but the essence of the profiles was usually pretty accurate.
Now, gripe - the Kemper often was not a match for the tone even with refinement. I get it's a plugin so maybe it's got weird stuff going on, but I think this is a more general problem with the Kemper capturing high gain tones. I often got a "too much noise" error for really high gain presets - more gain than i'd want, but it should be profileable. But even if it would profile, I found that while palm mutes might sound really good, single notes in the low register of the guitar could have this really ice-pick sharpness to the attack, where in the plugin the muted and unmuted notes sounded more similar and not as harsh...
Thing is, you can reasonably dial some of that out with some really keen EQ'ing before the amp in the Kemper. That's what I did with the profiles to try to get them into the same ballpark. What I often like to do is reduce Defintion and boost midrange to get a less harsh distortion that still chugs but can also handle leads. Here I found that it would really alter the tone away from the source too much. Almost all the profiles came up with Definition 10. That's a little frustrating to me, because the plugin's amp had controls for variable tightness and a bite switch. Most of the Petrucci presets had bite off and tightness at a very low setting. Even at the amp's "loosest" setting, Definition is 10 - no OD boost or anything in front the amp plugin. Anyway, I found in some case cutting some upper mids would help, other times maybe boost some lower mids. I wish the profiles would match the high-gain distortion characteristics a bit better, but then I'm also surprised by how well the profiles came out overall.
I also tried using some of the amp params, but felt like only sagging was working in helping the tone without getting further away from the core sound of the distortion. So I did adjust sagging on a few of the profiles.
In the end, I'm very happy with the profiles - not happy with plugin, but had fun with it. One of the problems I had with the plugin outside of the noise, gate, and double-tracker was the amp settings themselves were not very usable. This sounds a little bassy, so I reduce the bass - sound barely changes. wtf. You get better control with the studio EQ - but you only have 4 bands there. I find adjusting the EQ and overall tone in every way so much easier on the Kemper. The moveable mic stuff seems neat, but I'd rather have like 6-12 good cab sounds and pick out my few favorites than tinker with moving all kinds of different pairs of mic combos around. I tried not to pay attention to it, so I'm letting the presets dial that in.