Administrative Overhead: The version 2.x has very simple administrative process than Version 3. Modifications to 2.x standard are done easily by editing the change into the appropriate word processing document. In Version 3 changes need to be done to the computerized models, and the downstream consequences in the message structures need to be taken care of. This disparity comes into focus especially when introducing small changes into existing interfaces.
Message Size: The usage of XML as ITS and the adoption of ebXML as the wrapping mechanism for HL7V3.0 messages increased the message size hugely compared to a HL7V2.X message. The two layered wrappers consisting of ebXML wrapper and HL7 wrapper with duplicate elements contributed to the size.
Technological Barriers: HL7V3.0 has been built on RIM a decision which has been made in 1996. Technological changes and new architectural patters e.g. SOA make RIM which uses for e.g. UML look like a legacy hangover. The level of extensibility of RIM with well-designed ontologies for functions like computerized decision support which came with advances in clinical research is unknown and undefined.
Learning Curve: There is a very steep learning curve in understanding HL7V3.0 and there are no standard implementation and deployment guides available for starters. They need to traverse through the documentation available on HL7V3.0 site and the structure of documentation adds further complexity to the understanding of Version 3.0.
Inadequate RIM: The HL7 RIM contains an ad hoc mixture of health-specific concepts and domain-independent concepts. There are no classes to represent key clinical concepts such as 'diagnosis', 'problem' etc .HL7 proponents would argue that it is indeed possible to represent 'problems', 'diagnoses', etc. using RIM components. This may well be the case, by using suitable values of codes etc, but the general view of this is that HL7 RIM is far too abstract to provide a useful basis for the specification of health event summaries,
Multiple Tools: Multiple tools are used to design and build HL7V3.0 message specifications. For example the RIM is defined using UML, D-MIM and R-MIM using Visio, HMD using Rose Tree and the messages are in XML. The story boards are in formal English language and the application roles, triggers and interactions are in a PubDB. The usage of different tools in designing and publishing message specifications is expensive.