Lot of xc riders like Absalon use a very long stem and other (usually who ride with 29 er) a short one. I prefer short stem because i feel more confident during the turns and also in downhill. Anyway I think is not an easy decision.
I like the right sized frame with a 90 mm stem.
I'm at the larger end of most frame sizes, so most of the time I don't have a bike that is too long. I have ridden plenty of 'short' frames with a longer stem and have done just fine. Handling issues either way are usually solved within a few rides.
Specific to AR, I find the angle of the stem c/w the rise of your handlebars is equally important!. You can't ride for >10 hrs with hands that are numb!
I know some people prefer the smaller frame because smaller frames are easier to "throw around" on the trail. Probably more of a concern for an XC MTBer not so much an ARer. I am sure handling is different though. I am tall and have used a smaller frame for the past 6 years. I just upgraded to an XL 29er and interested to see the differences and make comparisons.
I think the frames are designed for specific usages. In xc bikes the frame is designed to have a longer stem, to perform better in the uphills. In a bigger frame changes not only the length but also the others parts.
I think the frame size has to be the right for your own height as suggested from the bicycles builders or biomechanics.
The other thing is a lot of Mtn Bike riders are weight weenies (or secret WW) so will go with slightly smaller frame to shave that extra bit of weight + what has been mentioned above.
I am also right on the cusp between frame sizes for the bike I ride and opted for the bigger size. Having had the opportunity to ride the smaller one set up similar to mine I don't regret my choice at all, and also mentioned above - riding for 10hrs or more on that smaller size would kill me for sure. I can see whipping around my local single track with it but anything more that a couple hours would be torturous.