I have to say I completely disagree with this. The guitar has a bigger part in a tonal quality if you're running your amp (mostly) clean, but by far an amp has a much bigger effect on your sound than your guitar has.
Sure, if you play a Les Paul and a strat into the same amp on the same settings you'll get a different sound, but you won't get a br00tuhl tone out of an H-H guitar through a Blues Jr - you'll get much closer with an H-H guitar through a Peavey 6505, for example.
I would look at changing speakers to get a darker tone. Something like Vintage 30's would be a good place to start. What amp are you using?
I get what you're saying, but comparing a Blues Jr to a 6505 is more a comparison of gain structure and character than tonal coloration. I play through an original 1st gen 5150, which is what the 6505 was modeled after, and a Mesa Road King II, and I can def make either sound "brutal" or clean or anything in between... But they take on decidedly different tonal characteristics depending on what guitar I'm using, what pickup im using on any givwn guitar, etc. Thus my statement that the guitar ultimately defines the subtle tonal coloration of the overall tone which <I> call "light and dark".
I will agree that choice of speaker cab can make a big tonal difference also. My main gigging cabs are original Sheffield equipped 5150 cabs or my V30 equipped Mesa cabs. Both sound great but they def sound different. I guess you could call the 5150 cabs a little "brighter", or the Mesa cabs a little "chunkier", but does that equate to "darkeness"? Totally subjective... But again, there are differences that go beyond just the speakers because i also have V30 equipped Marshall and Carvin cabs, and they both sound noticeably different than my Mesa cabs, even though all have V30's.
Again, I feel part of the issue here is trying to describe tone, and audio quality, with words - and written words at that. I really think coming up with specific audio samples of what one has and what one wants is the only way to get everyone involved in the conversation on the same page.