I've learned that I want the guitar itself to be as structure-ly sound as possible for best tone. I learned this from years of modding Squiers and then transitioning to Warmoths. I've noticed that the woods etc can kind of yield unpredictable results. You might get the opposite of what you expect and it might not be 'good' for you or it might just be different. However I established that I definitely need the guitar and all the components to be structurely sound to yield good plugged in tone. The thing not need sound like art unplugged, but I can get a general sense of what's going on with it unplugged. With the Squiers all kinds of crap was going wrong that would make it sound crappy to me. Hollow nut, then I'd change the nut and not necessarily do a good job, body and neck are all thin, bad bridge and saddles conduct like ****, bad tuners, change them and have it not come out perfect etc. All that crap would add up to make it sound kind of ding-y compared to my nice warmoths where everything resonates correctly and that translates into a nice amped tone.
This is the tricky thing.
My new belief is that there is an "inverse" relationship between what you hear unplugged and what you hear plugged in.
If a bolt on guitar with a thin neck and floating trem is resonating like crazy in room, its a pretty safe bet that the guitar will sound really warm when plugged in.
If a guitar sounds dark and "tight" acoustically, when you plug it in, there will be more treble/presense in the plugged signal.
If in-room resonance is caused by energy transferring from the strings into the body, that means there is less energy in the strings.
Lots of people are into the "light as possible" Les Paul thing. What you are getting is a mahogony neck glued onto a less dense piece of mahogony. It is more resonant in room, but this means less energy in the strings. A heavy/dense les paul should be less resonant in room, but keep more energy in the strings.
So I do think there is a relationship between what you hear in room and the plugged tone. A resonant guitar will be warmer/rounder when plugged in, allow you to turn up the gain, perhaps there is more fundamental tone when the presence is filtered away.
My current thinking is to avoid guitars with dead spots or inconsistency in resonance. As far as more or less resonant, I believe it can be worked around with pickup and EQ changes. I am interested in neck through construction for neck stability. I haven't heard a neck through that resonates like a typical basswood bolt on. (although they could be out there!)
Some guitarists want a lightweight guitar, either because they are gigging or they identify with the warmer tone. Some guitarists might want a denser sounding guitar, for more sustain, or in the case of neck through, maybe more stable neck.
On the internet, in general conversation, I think lightweight, acoustically resonant guitars have won the battle of public opinion.