Current CMS, regardless of their complexity and orientation, can be divided into two groups: one follows the MODx-concept, the other does not. The article describes the problems of building and development of WEB applications that are typical for standard CMS. The problems regarded in this article are relevant for all participants of WEB development. The problem of drastic changes to the interface is that it has to be constantly edited when the functionality is modified even if it is not related to this part of interface. This changing requires significant costs on the part of WEB developers and users. The problem of API continuity absence in standard systems is associated with the absence of atomic entity principle. The absence of API continuity leads to significant costs for CMS developing. The problem of connection between the different applications is due to the strong relationship between CMS components, which, in turn, does not make it possible to flexibly adjust the system to generate the content with the specific properties which are needed for joint applications. The problem of WEB application module conflicts is connected with unsystematic dependencies between CMS components. The inability to redefine the client part and the inflexible file hierarchy of standard CMS play an essential role in the problem of WEB application security. The scalability problem is primarily associated with the nonindependence of addresses on the site filesystem for standard CMS. The authors provide justifications for the application of the MODx-concept by a team of developers at the stages of WEB application design and operation to solve these problems.