Had a 2006 Stumpjumper S Works alum, then a Pivot Mach 5 and just recently sprung for the S Works Epic 29er. Honestly, the Stumpy had similar travel to an Epic 29er, but was more plush for trail riding. The Epic has a stiffer, more efficient suspension for racing.
We really push it on our extremely rocky, rooty, rugged trails, and the difference is noticeable. The brain is not an advantage in very technical and fast downhill riding. Even Specialized advises turning it off in these conditions. Even so the suspension is stiffer. You would have to try it to see what I am talking about. This only becomes obvious at high speeds through very rough terrain, esp. downhill.
Having said that I will probably never go back to the heavier Stumpy, even carbon. The climbing and level singletrack is just so much more enjoyable with the lighter bike, more efficient suspension, and 29er wheels. For me it makes the ride more fun in general. If you go this route, you should consider putting bigger rubber than the stock tires. After 3 cracks in the carbon fiber rear rim, I tossed the Renegade for a 2.0 Captain and it was a very good decision.
The suggestion to do a test ride is a very good one, but you must push the bike hard to get a real comparison. When I test rode one it was on the smooth hardpack trails of Calif., very different from our volcanic, forested trails at home. The stiffer suspension just wasn't as obvious as it is on our trails. That can fool you.