This article isn't going to enlighten you or give you the secret to running a top notch IT organization. And neither are most of the comments that have risen to the top. There is no magic wand. Anyone that tells you otherwise is probably selling something. There's just hard work and a commitment to excellence with the acceptance that there are certain things which are inevitable:
1) You're in business to produce a profit. You're not in business to procure, deploy, or worship technology. Technology is a tool. No different than a screwdriver or a machine press or a clock. It helps the workers be more productive and capable of producing a profit. Nothing more. Nothing less. Used well, technology is power. Used unwisely, it's an anvil around your neck.
2) Organizations are groups of people. People in groups don't communicate well. People one on one usually communicate very well. Whenever you get a large enough group, there will be miscommunication and that thwarts most "techniques" or "methodologies" engineered to negate this effect. The sooner you realize that you can't engineer away humanity, the sooner you'll be successful in using one on one relationships to get most of your wins. ALL organizations will NEVER be in sync at any given time.
3) No matter where you work, there will be a bell curve of capability and skill. You'll have a few rock stars, most people will be in the middle, and there will be a few truly aweful people. It doesn't matter if it's Google or the Army or AJ's Nails and Hair. No organization can attract the best and brightest all the time for all needs. So even if you have good processes and good relationships, they won't always work and you won't always get good results. The best you can do is work hard to provide the best you can and accept the fact that not everyone you are working with is capable or motivated to do the same. Stop complaining and do what is reasonable to solve the problem. That will bring you the most success. And happiness. Read this again, and then lower where you think YOU are in the bell curve.
4) People are relying on you to guide them and help them to make informed and intelligent decisions. To them, what you do is scary and expensive and magical all at the same time. Keep the previous 3 points in mind on how they will present their problem to you and respond to the solution that you present to them.
I've been a CIO for everything from startups to publicly traded companies to companies I've founded. The principals don't change. Just the budgets and egos.