Based on my experience, a functional organization seems to work well in large companies. Yes, a disadvantage is the creation of silos but that can always be resolved. Having an IT, marketing, finance, quality, manufacturing departments allows the members of those departments to specialize in a specific tract within that department. Therefore, when it comes to working together, you can ask the department lead for a certain skillset and they will have a person qualified to take on the project. One issue with functional organization is getting each department to understand their boundaries. If you have a common goal, then it is easier to work together but each department should not interfere into other department responsibilities. Each department should get to know each other and know their responsibility and then move on from there.