http://www.elitefitness.com/forum/showthread.php?t=375215 = Big Thread - it's linked in the stickies
It's about applying weight to the system (what makes the squat and dead so good). You can't use as much weight with incline and the 5x5 is about getting big and strong. If you want incline do it on Wednesday or set aside a 4 week period to pound on it and some other accessory work afterward.
All that said, there's nothing to stop you from substituting it in for flat bench (move flat to Wed). Maybe it will be better from an aesthetic point of view but most people will find themselves with less results (not sure how measurable it will be but if you did it for enough people, you'd see it in the stats).
Keep in mind, it's not geared to BBers, it just happens to be a good general program that produces a ton of muscle - generally a lot more than or every bit as much as any other program you can throw at it. Most people find that putting on muscle is the biggest challenge and not refining shape (what is actually addressable and not just set in stone like biceps peak or calf insertions). If you train properly, it's also pretty rare that people find major aesthetic issues - most have been very happy to see arms and rear delts respond nicely without any direct work.