This essay by Paul Graham (YC founder) from back in 2007 has been doing the rounds recently (trending on HN), and it struck a chord with me because of the following extract and the new project with which I am involved - YunoJuno - www.yunojuno.com.
YJ is founded on precisely this belief - that certain 'craft skills' (designers, developers, ux etc.) are not interchangeable, and that the success of a project is very largely dependent on the specific individuals involved.
To that end, we want to create exactly the kind of relationship that Paul outlines below - "Maybe we could define a new kind of organization that combined the efforts of individuals without requiring them to be interchangeable."
It's a vision we share, and one that I hope YunoJuno will be a part of (specifically the part that looks after the individuals). If you have a skill, and you want to treated as an individual, but to feel part of something greater, then head on over and 'Join the Family'.
One of the defining qualities of organizations since there have been such a thing is to treat individuals as interchangeable parts. This works well for more parallelizable tasks, like fighting wars. For most of history a well-drilled army of professional soldiers could be counted on to beat an army of individual warriors, no matter how valorous. But having ideas is not very parallelizable.
And that's what programs are: ideas.
It's not merely true that organizations dislike the idea of depending on individual genius, it's a tautology. It's part of the definition of an organization not to. Of our current concept of an organization, at least.
Maybe we could define a new kind of organization that combined the efforts of individuals without requiring them to be interchangeable. Arguably a market is such a form of organization, though it may be more accurate to describe a market as a degenerate case—as what you get by default when organization isn't possible.
Probably the best we'll do is some kind of hack, like making the programming parts of an organization work differently from the rest. Perhaps the optimal solution is for big companies not even to try to develop ideas in house, but simply to buy them. But regardless of what the solution turns out to be, the first step is to realize there's a problem. There is a contradiction in the very phrase "software company." The two words are pulling in opposite directions. Any good programmer in a large organization is going to be at odds with it, because organizations are designed to prevent what programmers strive for.