What guitar? Bridge/saddles, nut, strings, pickup type, pickup placement, pick material, cable length, buffer... all of it plays a role (in addition to concerns about the internal electronics) and most of it can be tweaked.
Most dual humbucker guitars are darker than most three single coil strats
I am curious as to what guitar is so dark
A long cheap off brand guitar cable can bleed highs off
I'd also start exploring the EQ on the amp, too. Most people just set the EQ on an amp to be the same for every guitar (and the same on any amp, too). Other than that, I'd suggest an EQ pedal, or a drive pedal with the gain set at 0 (but used as a tone control). Before I started swapping out pots, I probably would look at pickups, too- pots can certainly get 'peaky' and affect the sound in a strange way if the value gets too high.
Do you set your amp differently for different guitars?
Maybe I'm just lucky or something, but I've got like seven guitars - all with wildly different pickups ranging from low output singles to high output humbuckers . . . but they all seem to get along with the same amp settings. At most I might tweak the bass or treble a notch when switching.
Do you set your amp differently for different guitars?
The 5-band EQ on my amp is foot-switchable, so I set it up for a mid-boost for those pickups that need a bit of help.