When performing analysis between an existing system (AS-IS) and its desired future state (TO-BE) you could take into account all aspects/dimensions.

Having said that, I realize that this approach may not always be practical nor necessary.  So you should probably determine the focus of your gap analysis by answering the following questions:
- What are they key characteristics of the system?
- What do you know about the existing system?

For example, if your system is workflow centric then it would probably be very beneficial to focus on the differences in workflow and document them by creating a workflow diagram which focuses on the differences.

On the other hand - if the only documentation you have of the existing system is a list of requirements then you should start by identifying he requirement gaps.

So getting back to the domain model....

If you are doing a Domain Model gap analysis focus on and document the following:
- Differences in business entities (new entities, entities no longer needed, etc.)
- Differences in entity relationships (diffs in types of relationships, diffs in multiplicities, etc.)
- Differences in attributes for a given entity (new attributes, attributes no longer needed, etc.)
- Differences in methods/behavior

Hope this helps!
- Adrian