1) Exchange is licenced by server deployment + user licences, while GroupWise only incurs user licence fees. This can be rather costly if you decide to deploy a branch office email server for a few staff. For GroupWise the cost is going to be just the user licences if you are a NetWare or SUSE OS user, while Exchange will need a MS Server licence, an Exchange server licence and user licenses.
2) Exchange uses a SQL database for its email store this offers many useful feature but has the weakness of being unencripted so any administrator of the system can read the emails held within the database. GroupWise has a less flexable data store, but all messages are held encripted at all times. This includes when they pass POA MTA and MTA MTA.
3) With Exchange using an SQL store it consumes far more storage space for a given set of emails than GroupWise which compresses messages.
4) A GroupWise server indexes just about every item it stores in its database with PDFs being supported in the next release. Exchange also has such a feature, but articals indicate that it can increase the database size by between 10 and 30%. This is often over looked when someone quotes for a GW to Exchange migration project.
For items 2 and 3 you can purchase third party tools to deal with the issues - for a true comparison of product costs these should be included. For Item 4 you need to add additional disk space.