The fact that the Kona has hydraulic brakes would give it a big leg up in my book.

I happen to have a Muirwoods 29er, so I can tell you a lot about that. The stock version was quite heavy (about 30 pounds). I don't know how that compares to the other bikes you're looking at. The Alivio stuff shifts surprisingly well. The stock brakes aren't especially good. Mine came with Avid BB5. A friend of mine got a 2009 which came with the Hayes. Neither one of us liked the brakes. We both upgraded to Avid BB7's and have been very happy with that decision. The stock handlebars are absurdly wide and quite heavy. That's a cheap place to lose weight. The stock brake levers are uninspiring -- another thing that can be fixed quite cheaply. It will fit 29x2.0 tires with fenders, but just barely.

I've had a lot of fun tinkering with my Muirwoods. It's a fairly versatile bike. You can see a bit of the history of mine here. Every summer (when the rains stop) I consider getting rid of it. Every fall (when the rain start again) I'm glad I didn't. I've put about 4000 miles on it in two and a half years, and it's stood up to a lot of abuse.