In February 2012 I switched from a HT 1999 Stumpjumper M2 to a FS Giant Trance X2 (i.e. they are both XTR equipped). I have been riding mountain bikes since 1981 and have had the Stumpie since new. I am a moderately skilled rider who is losing his nerve as he approaches Medicare.
I love the comfortable ride on the Trance and the ability to ride some really rough terrain with a lot of control. I rode the Trance over a thousand of miles between early February and late June - all of it in San Diego county and all of it on pretty technical single track. Lots of big rocks, big drops, sharp little creek beds, and really steep rocky climbs. The suspension works exactly as advertised.
However -
I am now in the Pacific NW for the cooler summer and am riding my old Stumpjumper HT more than the Trance FS bike. In the very tight and narrow, windy, single track where the path between the trees is often only inches wider than the handlebar, and there is a 150 degree turn every 20 yards, I like the agility of the Stumpjumper. I also like the lightness and quickness of the HT Stumpie on many of the long fire road climbs that we have around here. The extra 8 pounds for the FS and strength of the Trance is not needed in many of the locations I ride here in the NW.
The important point is the need to understand your riding style and location before you decide on the bike you want to buy or build.
My next bike will be a light HT 29er. I rode down Noble Canyon (fairly technical with some serious rock gardens and drops) in San Diego with a guy on an HT 29er and talked to another who had just come up the canyon. They both felt the HT 29er had the feel of a 3" to 4" travel full suspension 26er but the ability to more easily roll over a lot of obstacles due to the 29" wheels. They were both much better technical riders than I and sure made it look easy and comfortable on those HT 29ers.
I just have to convince my wife I need a fourth mountain bike!