projects include integration between several applications, this becomes the necessary evil going forward. Changing to interoperability in such cases takes a lot of effort in terms of both cost and time. In such cases, integration becomes the norm.
This may not be the case if the organization has a strong technology strategy and its main objective is to keep integration at a minimum.
Organizational Willingness and Ability to Invest in Development, Testing, and Maintenance
Resorting to integration instead of interoperability substantially increases the overhead of development, testing, and maintenance. Design/code changes require a lot of testing. When a number of applications are integrated, a complete cycle of testing is required to ensure nothing is broken and everything works, so business can continue as usual.
Higher degrees of integration will mean higher maintenance costs for the organization. If an organization is looking at cost saving, it should go toward interoperability rather than integration. If it chooses to outsource or buy from a third-party vendor, interoperability becomes an important quality to consider during the selection of the potential candidate.
On the other hand, if it is the policy of the organization to have its own development center due to security or privacy reasons and the existing applications don't cater to interoperability, integration might be a better option.
Nature of the Core Business
Organizations with a core business that provides services to the general community, like banks, financial institutions, and other retailers, are more likely to have legacy systems. For these organizations, it is harder to get the application to interoperate, and normally some amount of integration is involved when a new application is implemented.
If the organization is a supplier of applications or application suites that are purchased and implemented either as standalone or integrated solutions by other organizations, the approach to interoperability can be radically different. The organization can actually build interoperability into its products. This does not mean that these applications cannot be integrated if need be. Rather, these organizations have an edge in selling something that can be used virtually "out of the box" if the customers desire to do that.
So what is the best implementation for an organization? There is no one, best way. An organization can choose either to interoperate or integrate, or even partially both. It depends on the nature of the business, the technology strategy, and the long- and short-term goals of the organization. It definitely is not a decision that should be made in a split second, but something that should be carefully determined by the stakeholders.