In my opinion, The most important challenges facing the design of the organizational structure are the agility of the organization's aligement to the digital transformations of the enterprise.
Sumantra Ghoshal and Christopher Bartlett have recommended that organizations should move beyond strategy, structure, and systems to a framework built on purpose, processes, and people. They reckoned that a fatal flaw of the traditional strategy–structure–systems construct—which of course owes to Taylorism and scientific management mindsets—is the intention to minimize the idiosyncrasies of human behavior. They recommended (i) less emphasis on following clear strategic plans, and more importance to defining engaging purposes; (ii) less focus on formal structures, and more attention to effective processes; and (iii) less concern for control through systems, and more appreciation of capabilities and perspectives. If so, it follows that the most important challenges facing the design of an organization's structure have to do with the degree to which it helps accomplish purpose, in support of which it best leverages people by means of the most efficient and effective processes.
Any organisational structure has its elements (people and other resources) to be interrelated and behave among them through all processes that that structure will be built for, ensuring with the greatest effectivity and efficiency (that is, performance) the realisation of outputs and other objectives (or purposes). The challenges are still related to those ingredients and may vary according to the situations at hands, knowing that these situations may vary in various degrees and environments time after time. So, there is a need for the combination in right doses of rigidity, flexibility, resilience and sustainability.