I've talked to engineering executives who agree, "I've read all of Joel's stuff", but then fail to implement his ideas at a concrete or abstract level. I don't know why.
Joel's advice is best taken at the founding stages of a company. It's extensive, and it's structural, and it needs to be part of the company's foundation. If you're the one group or division at a large company that "goes rogue" and operates on Joel's principles, even if you have the political clout to do so, you're painting a target on your back. You're taking a huge political risk. Maybe it pays off. Maybe it doesn't. At any rate, very few people reach executive status at established companies without a keen understanding of internal politics, and the constraints it imposes.
I'm not defending politics, of course. I'm just saying politics exists, and it's a powerful organizational force.
1) A whole lot more work and responsibility will come your way.
2) Other divisions will want to emulate your success.
If you are not successful, then yes I think sticking your neck out in a big organization is a good way to lose your head. The thing to remember is that if this organizational change is well executed then your likelihood of success increases.
3) Other divisions will get envious and seeing no way to emulate you they will try and stab you in the back or in other ways sabotage your work.
Maybe they will fail, if you're that good and/or have great political skills. But it's definitely something that might happen, and you have to be prepared for, and potentially prepared to lose.
Another powerful force to consider is employee morale. Employees tend to settle into a routine and resist change to that routine -- even if it's nominally better for them. You'd be surprised at how powerful a force this is. I can almost guarantee you that if you went to any big company with an open-layout, cube-farm floor plan and proposed that everyone be given their own office, a significant percentage of those employees would grumble about it. It sounds silly to think so, but it will happen. People fear change. They tend to read into it. They think it's a harbinger for more sinister or scary things to come. Loss-aversion is very real and very strong.
Of course, the upside to making big changes is the chance at big success. If you turn around your division, or if you're the one division outperforming all the others, you're a hero. And other divisions will follow suit. That's a wonderful thing. But the risk that that won't happen, and that your changes will backfire or be scuttled in some way, is every bit as real as the potential upside. When faced with that calculation, and especially when taking into account the stability of a very nicely paying and high-ranking job, a lot of managers and execs will opt not to rock the boat.
Again, this is not a defense of change-aversion. It is an explanation for why you don't see more change in established firms. The vectors of big change tend to come from outside: a new CEO, a new executive hire, or the formation of a new business or division. In those circumstances, the organizational and psychological frame is oriented towards change, rather than towards the preservation of the status quo. The person leading the change has a clear mandate to do so. In other, more day-to-day circumstances, the mandate is less clear and less easily secured.