I am looking at the Fender American Stratocaster, and I want to buy it in the 3-tone sunburst finish. However, I can have two different neck choices: Maple or Rosewood. What are the pros/cons of each neck? Is there even a difference? Does one sound better than the other? Play better?
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Personally, I think it's subjective. I tried both Maple and Rosewood necks/fret boards when I was looking for my strat, I couldn't notice the difference.

I got a maple neck/fret board because I preferred the look.

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Maple is a more trebly sound, whereas rosewood gives a tiny mid boost. You notice cosmetic damage/dirtying on maple easier, but many people (myself included) think that it looks cooler, dirty or not. Honestly, on an American Strat, either way you're getting a top-quality instrument.
As others have said, maple is a bit brighter, and there is definitely a different feel to them. You should without a doubt try each before you pick.
I doubt anybody here could tell the difference between the two just by listening to them. Likewise nobody you're ever going to play to will ever be able to tell. Hence, go for which ever you think feels best or looks best.
i'm a rosewood kind of guy.

banana maple is THE ****, but I think it's mad expensive
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