Currently the Dynamics CRM product does not support the use of ILMerge. This limits the development of plug-ins where you want to use external libraries to extend your business logic. As there are no other alternatives to add external libraries into Dynamics CRM, developers are not able to use the logic of external libraries in a supported way, unless they use ILMerge.
Numerous times we receive the error message "Unable to load plug-in assembly" when importing solutions or updating our plug-in assembly with the plug-in registration tool. As this is an intermittent error, most of the times we are able to upload our plug-in, but once in a while we receive this error. According to Microsoft support, the issue lays within the use of ILMerge. To quote MS Support: "Once the use of ILMerge was never been tested by us and once it’s precisely the point of contact between you and other affected customers, we believe that ILMerge is the cause of the intermittent behaviour."
Therefore we would like ILMerge to be natively supported by the Dynamics CRM product!