Hi @Teepi!
There are quite a few questions in your post here, so I hope I get to most of them. First, you can absolutely have distinct Zebra preset patches in MG2. It doesn’t take any more CPU power to run a Zebra in MG2 compared to outside in Abelton in my experience. The thing is then you have access to the clean channel as well, and don’t need that rack setup. You just send the audio output to your looper directly. You just need to have a controller (pedal) connected to the “master mix” to be able to decide what should be passed on.
As I mentioned above you can absolutely change patches on MG2 in plugin mode. You just need to see to that your pedal CC.s (Program Change) are relayed to the AUDIO track as per the above description. You dont need to adress that inside MG2.
And yes, MG3 is on its way, and I’ve been most fortunate in that I’ve been involved in a small part of the testing process. I can’t however tell you anything in terms of release dates and status yet. All that is going to come up on the roadmaps page in due time, and if you haven’t already: sign up to the mailing list to be sure to get all the info on that.
Yeah, breathcontroller is a great addition for many instruments. I am using the TEControl BBC2 everywhere, but there are of course a few options. But I agree, the combination of MIDI Guitar 2 with a breath controller and a well written instrument is giving us incredibly realistic results nowadays. 
