For me I find there are great sounds to be had with all the softwares if they're used "well" if you have the right gear and the right room, live mic(s) on an amp is great. Using the virtuals for me is a challenge at learning to use different tools to accomplish a familiar job. The more I use them, the more I like the results I get. I do plenty of live amp mics in many situations, but not all.
The TH2 is very powerful and capable, but I find I prefer the results I'm getting with Amplitube 3 Free to which I've added a few amps, cabinets, and mics. I also own an old ART SGX 2000 Express which I use as my live rig. I've always had excellent results with direct out of this and then sometimes adding a virtual cabinet. A lot depends on the kind of sounds you're looking for as well
Even with all the sophisticated modeling, it's sometimes hard for the ear to remember that the virtualization is being played back in full range monitors, not guitar speakers, so getting it to sound as though it's coming through guitar speakers is a key. They do not have the high end that studio monitors do. So I find the virtuals are consistently too bright and rolling off the top quite a bit near 4k or so with a low pass or shelving EQ makes a world of difference...
Input... Yeah that's a tougher one. An instrument input is the best choice if you have it but what impedance value is has is still to be questioned by each user to their own personal taste... Matching a guitar to an amp is much the same thing as some guitars are hotter and some inputs are more sensitive...
In the end, we're making art... If you carve a sound you like with your choice of tool, it works! Setting an amp is as unique virtually as it is in the physical world...
Keni