I have a 2010 Giant XTC 29er1 and a 2009 GF Rig,although the Rig is heavily modfied with a Shimano SLX M665 drivetrain making it a 2x9. I also upgraded on the brakes on the Rig to Elixir R's and changed the front rotor to a 185mm disc. The stock saddle was upgraded to a leather suspension saddle.
My XTC 29er1 is also modified,I'm running a 203 mm rotor in the front. I swapped out my my Avid rotors for Shiman RT 76 floating rotors. The brakes have also been upgraded to Code 5's. I changed the stock seatpost and use a leather suspension saddle.
Although both bikes aren't stock,especially the Rig,I feel qualified to write about the differences between both bikes.
The XTC 29er can definitely hit bigger stuff than the 2009 Rig,note that the 2009 Rig has 80mm of fork travel versus the 100mm found on the 2011 Rig. However despite the differences in fork travel I believe the tapered headtube and the 15mm t/a on the XTC29er1 are responsible for this effect.
The frame on the XTC 29er1 also feels more rigid than the frame on the Rig. The stock crankset that came with the Rig was definitely soft,the bike felt more rigid on landings after changing out the crank to Shimano's M665.
The only real disadvantage of the 2010 XTC 29er1 versus the Rig was the rear triangle. When I had the Juicy 3's on the XTC 29er1 would simply make a howling noise upon application of the rear brake. When I upgraded the brakes on the XTC 29er1 from Juicy 3's to Code 5's the brake noise turned into vibration. I think this vibration set in because the Code 5's have far more grip/stopping power than the Juicy 3's and transmitted this energy directly into the rear triangle. I ended up using Shimano floating rotors and elimanating the vibration,however I still have the noise.
By comparison the only noise problems I've had on the Rig were the BB7's,for some reason the BB7's howled like wolves or dogs baying at the moon on that bike. After changing out the calipers to Elixir R's the howling went away.
For 2011 Giant made some major changes on the XTC29er1 and went with Shimano for the brakes and went to a 10 speed drivetrain. If I'm not mistaken I believe that Giant has also beefed up the rear triangle to attenuate brake vibration/noise.
Overall I'm pleased with both bikes but would have to say the Giant is simply a more stiffer and burly bike than the Rig.