Let me try to answer this tough question:
Level 1:
If you are after the correct timbre -- mainly its the amp and more likely the speaker cabinet qualities and speaker. After that, its your pickups and the design of your guitar in terms of construction, wood, hardware and strings.
Level 2:
If you are after expressiveness -- mainly its the guitar specifically the unique marriage of distinct pieces of wood. After that, its enhanced by the responsive qualities of the amp and the speaker cabinet.
Level 3:
Great expressive guitar and 'tonefully' touch sensitive amp with correct speaker combination. This is the ultimate set up. Unfortunately, very few get to this level. I would say in Manila only less than 10% get to level 1. At level 2, less than 5%. At level 3, thats me and a few others.
Honorable Mention:
Pedals are indeed fun but detrimental to the whole sound. So, use sparingly in combination with your Level 3 set up. What I mean by sparingly is one or two pedals in front and one or two pedals in the FX loop (either modulation, delay or reverb) and make sure you can switch it out.