Funny, the OP was looking for some help on choosing a bike and it seems to have turned into a pissing contest between Trek supporters and Trek haters, Kona supporters and Kona haters, etc.
To the OP, I'm pretty sure that in the $2000 to $3000 range you're going to get a high quality bike no matter what brand you wind up choosing. So, fit and function would be the two main things you want to consider. First thing that you want to deterimine is what type of riding you will be doing: downhill, XC, freeride, etc. That will at least narrow your search down. Secondly, get on the bikes and ride them. Go with whatever feels comfortable. If you're not comfortable on the bike, you won't ride it and you'll have wasted a good amount of money. Trek and Kona are both good brands, especially in the price range you are looking. I wouldn't rule out any of the other brands either. If your price range was more limited, it might be easier to steer you towards a bike that provides good value. At the price point that you are considering, you have a ton of great options.