Design Pattern for Undo Engine

I think both memento and command are not practical when you are dealing with a model of the size and scope that the OP implies. They would work, but it would be a lot of work to maintain and extend.

For this type of problem, I think you need to build in support to your data model to support differential checkpoints for every object involved in the model. I've done this once and it worked very slick. The biggest thing you have to do is avoid the direct use of pointers or references in the model.

Every reference to another object uses some identifier (like an integer). Whenever the object is needed, you lookup the current definition of the object from a table. The table contains a linked list for each object that contains all the previous versions, along with information regarding which checkpoint they were active for.

Implementing undo/redo is simple: Do your action and establish a new checkpoint; rollback all object versions to the previous checkpoint.

It takes some discipline in the code, but has many advantages: you don't need deep copies since you are doing differential storage of the model state; you can scope the amount of memory you want to use (very important for things like CAD models) by either number of redos or memory used; very scalable and low-maintenance for the functions that operate on the model since they don't need to do anything to implement undo/redo.

Most examples I've seen use a variant of the Command-Pattern for this. Every user-action that's undoable gets its own command instance with all the information to execute the action and roll it back. You can then maintain a list of all the commands that have been executed and you can roll them back one by one.