again, not GUE, but been active in sidemount for about 7 years now, cave for almost as long. With GUE, from what I understand the number one thing that has turned them off to sidemount is not being able to donate the primary regulator hose 100% of the time. This is just not possible without a HP crossover between the tanks which are expensive and impractical, especially for true sidemount exploration because it ties the bottles together. That hasn't been fixed, it has been screwed up with the UTD manifold, but the problem there is you have to constantly shut one bottle off to the manifold when you do switches which makes the gas switches actually much more difficult because you have to reach back and turn a bottle on and off instead of always having that secondary right there.
regarding the manifold, the reason they don't condone independent doubles is the same reason, you can't donate your primary 100% of the time. The isolation manifold isn't really part of the discussion because it doesn't change much and it's your decision of whether or not the risk of that manifold valve leaking is greater than one of the tank neck o-rings, the burst discs, or three of the crossbar o-rings on the same side. To each his own, I dive independent doubles if given the choice.
So you can argue for sidemount that you can have two long hoses, but with right handed regulators that means the long hose is cross under one of the divers which can get caught up in things, especially stage bottles since GUe hangs their bottles quite low, and it also increases the risk of pulling the regulator out of the other divers mouth because it has that much more rotational torque on the mouthpiece. Not good. Donating from the left tank only really works with left handed regulators, which mean you have to have the regulator coming straight up to your mouth. Fine, except in really nasty sidemount passaged where that hose getting caught on a rock can rip the reg out of your mouth, so you need them crossed over your neck. Again, can be worked around with non-direction regulators, only problem is the only reliable ones on the market are Poseidons. GUE has a think against upstream regulators, so the servo valve on the Jetstream and Xstream rules them out, and the Cyklon uses an IP of 165 which is much greater than any other reg on the market and as such has its own limitations.
Figure out a way to get a pre-first stage cross over between the two tanks practically, or figure out a hose routing that works for both long hoses so they don't cross each other behind the neck or across one of the divers, and you'll make JJ a very happy person. Until then, doubles win.