Perhaps we will have a Tone Talk board in here someday, but until then, here goes.
I am setting up my rig to be running directly into the PA and have found that there is a VAST difference in sound according to guitar construction. Most of my twin humbucker guitars have EQ set up very similarly, I just adjust the gain & EQ to taste with differing pickups. But, there is a vastly different sound coming out of my RG (which also has two humbuckers)
Ibanez RG model = basswood body, 3pc Maple neck, HSH config (Dimarzio Evolution / Ibanez INFS3 / Alnico 2 Classic), Floyd Rose trem with a big brass block upgrade.
Had to crank the bass on this guitar and cut the highs a bit, just to give her some 'body' in the mix. Also had to bump the distortion a bit.
Ibanez AR model = mahogany body w/maple cap, 3pc maple neck, HH config (SD Sh-4 JB / SD Sh-2n Jazz), standard Tune-o-matic bridge w/stoptail.
Bass and highs bumped up a bit, mids cut.
Gibson Explorer = Korina body, mahogany neck, HH config (both Gibson PAFs), Kahler Trem.
Just add a bit of gain for the low output PUs, EQ is about the same as the other HH models = Boost lows, cut mids, bump highs just a bit.
Epiphone Korina V = not a full Korina body, it's a white mahogany body wrapped in Korina, but sounds very similar to my Explorer, mahogany neck, HH config (SD Sh-1 / SD Sh2n Jazz), TOM bridge w/strings routed through the body (no stoptail).
Exactly the same settings as the Ibanez AR model. (has nearly the same pickups too)
I don't know what makes the RG sound so thin, maybe it's the Evo pickup, maybe it's the basswood body, maybe it's the bolt-on neck, maybe it's a combination of all of that.
The fact that I had to turn up the gain on the RG made me wonder if I had a loose solder joint in there somewhere from when I installed the PUs, so I remelted all the connections again, with absolutely no difference in sound.
So, it's all working out fine, I have a bank of patches for each guitar, I just thought this EQ difference was worth mentioning. When asking others for their 'patch settings' keep in mind that your rig may sound VASTLY different from somebody else's.