I did extended test-rides on the '09 Giant Trance X2 and '09 Specialized Stumpjumper FSR Pro and ended up buying an '08 Stumpjumper Pro.
The Hayes Stroker Trail brakes on the Trance X2 were the worst hydraulic disc brakes I've ever ridden; tons of noise and very poor modulation/control. In addition, I wasn't terribly impressed with the Maestro suspension. Coming from road bikes, I'm very sensitive to pedal-induced bob. The X2 didn't bob as badly as some of the full-suspension bikes I've tried but it was enough to annoy me. I think that part of the problem was the RP2 shock, which seemed to have only two settings: Bob and Lethargic. An RP23 might have allowed me to adjust the ProPedal platform damping to the point where the Maestro suspension would have worked better. An RP2 shock with the "low" compression tune might also have worked better for me than the "medium" compression tune on the shock I rode. Finally, the Fox F120 RL fork seemed a bit harsh. It was the only fork I've ridden that had the new 15QR axle, but I couldn't tell that made any difference in the ride. Tuning on the F120 RL is limited to rebound damping, air pressure, and lock-out threshold adjust. When traveling down trails that looked flat, it seemed that every minor surface imperfection was transmitted directly to the handlebars. I actually like a fork that feels a bit firm, but I thought the F120 RL on the Giant Trance X2 was just a touch too firm. I don't really like Shimano's RapidFire shifters, so the Trance X2 lost a couple of points there too.
I found a great deal on an '08 Stumpjumper Pro; it ended up costing about as much as the '09 Trance X2. The Brain-equipped Stumpjumpers seem to be a bit of a "Love It" or "Hate It" design. Personally, I love the fact that the Stumpy feels exactly like a hardtail when climbing! But that's not necessarily a good thing for some: while the design is an extremely efficient climber, it tends to be a bit rough over small, slow-speed hits. It's very much like a hardtail in that regard. You can soften up the shock to minimize this characteristic, but eventually you'll start to feel some bobbing. It never gets as bad as the Trance X2, though. The nice thing is that the Brain is truly a set-it-and-forget-it design; when descending, the inertia valve opens up and the ride is fantastic! Like the Trance X2, the Fox F120 RLC fork on the Stumpy tends toward "firm" rather than "plush" suspension action. The Fox Talas fork on the '09 Stumpjumper Pro was probably the best fork of the three. The F120 RLC on the '08 Stumpjumper Pro was nice because you could use the low-speed compression adjuster to tune away some of the small-bump harshness that seems endemic to the F-series forks. I wouldn't call either the F120 RLC or the F120 RL "plush", but I found I could tune the RLC to the point where it didn't annoy me. Finally, the Magura Marta disc brakes on the '08 Stumpjumper Pro were fantastic! Good power, excellent modulation, and no noise!
Of course, despite the fact that prices were nearly the same for me the '08 Stumpjumper Pro and the '09 Giant Trance X2 really aren't in the same category. Retail on the SJ Pro is $1700 more than the Giant, so you'd expect it to be a better bike. In comparing the '08 Trance X2 to the '08 Stumpjumper Comp, I think you'll find that the '08 Stumpjumper has: better brakes (SJ=Juicy 5, X2=Hayes Stroker Ryde), a better shock (SJ=Specialized/Fox Triad, X2=Fox Float R), and a better fork (SJ=F120RL, X2=F120R). The '08 SJ Comp also has SRAM shifters, which I prefer to Shimano. The '09 Giant Trance X2 has upgrades to the fork, shock, and brakes so it's a more comparable to the Stumpjumper.