Issues for Smaller Organizations
The primary issue is the complexity of the system and the dependency on outside resources to help address questions or concerns you may have. While there are a ton of great resources out there, the issue is the cost associated with using them. If you have a complex membership structure or need to manage multiple tax ids or accounts, the system becomes very hard to achieve. The reporting capabilities, while nice appear to have discrepancies in the results returned based on corresponding reports that were created, which leads to trust issues in what is being returned. The web version has promise, but it's apparent when working solution providers that most of them still have a client-server mentality, and this migration will to the cloud is and will continue to be bumpy for the foreseeable future.