Finding a great Tone
What does affect the tone on an electric guitar? 
Well what I found is that tone is effected by many factors. Tone can be affected by the type and quality of wood chosen but it is also affected by the pickup type and its height, pickup wiring combination, position to the strings, string gauge, plectrums material, plectrum size, plectrum stroke angle, the hold strength of the plectrum, fingers touch, amplifier models, stomp boxes, effects, speaker size and types, cabinets, location of speakers in the room, height from floor, distance from walls, distance from corners, even the absorption of materials substrates as paper, paints, finishes, etc. etc.

The skill of a player is of course a great factor of this but it must be also said, that tone is subjective to each person and what sounds right for you might not sound right to others.Have you had this happening to you? You practice your favourite song, find a great setting on your amp and loose yourself in space and time for hours (drug free I might add, LOL). At the end, you feel really great! You look forward to playing it again the next day. So, the day comes and you made sure that the settings are just the same as before but on strumming the first chord it sounded VERY different. Well... it’s very likely that one of the reasons mentioned above is the culprit, or maybe your partner just rearranged the room for you. Now you are back to square one and waste countless hours trying to regain that lost tone. You may find helpful that if you take a break from listening to your guitar... just for few hours... the tone will sound again different when you will re-listen to it.
It is for this reason that it is a good Idea to record your playing and make the necessary adjustments after you heard the track back over few days; Doing this, it will also highlight you skills, strengths and weaknesses.

I would recommend that you get yourself a decent band equaliser and make additional adjustments to the tone, in addition to using the guitar tone pot. A great tool for tone making is Guitar Rig 3, by Native Instruments; a virtual multi amps and stomp boxes that gives the guitarist a vast array of tone generation