After setting up my G-System it sounds like it's coloring my tone. How do I avoid that?
The G-System was designed to provide as uncolored a signal as possible; ideally going through G-System should sound just like plugging straight into your amp. A completely transparent pedal/effect unit is however an impossibility - as soon as your signal passes through a circuit it will unavoidably be changed. The trick therefore is to try to color as little as possible.
The most important thing when dialing in your G-System to be as transparent as possible, is to set up the levels in G-System perfectly. Even the slightest change in output volume will be noticed; not necessarily as a change in volume, but as a change in the tonal characteristics. The human ear won't hear a 1dB volume increase, but it will perceive it as an increase in high-end content. Similarly a 1dB volume attenuating will sound like there's less high-end sparkle to the sound.
This means, if your G-System levels aren't set up exactly as loud as when you plug directly into the amp, your ear will perceive that as if G-System is adding or removing high-end frequencies, which means, getting the G-System levels set up perfectly will fix most perceived coloration "problems".
For setting up your G-System levels we can recommend the paper "Understanding and configuring your G-System" by Laird Williams.
There are however a few guitars that may sound slightly different when going through G-System than when plugging straight into the amp. This coloration is due to an impedance mismatch between the pickups compared to the G-System input. This is in essence what the new input circuit in the G-System Ltd and all newly produced (regular) G-System models addresses.
Owners of earlier G-Systems without the input modification who are looking for a similar solution, can achieve a similar result by placing a buffer between the guitar and the G-System instrument input.