I'm not sure how to describe this, but it was a random idea I just had that I thought I'd suggest.
Basically, I've just realised that I have on my desk in front of me an army list (hand scribbled) for 1500pts of Orks with a "modifier" addon to take it up to 2000pts, and an "anti-heavy armour" "modifier" that uses either of those base lists and swaps weapons and troops in and out to get a more anti-armour list.
Now, you could easily do all of that just by using the tool (after-all, if it is an easy point-and-click interface then you can play around and just not save your changes), but would it be a good idea to allow for a similar setup of an army and then a "modifier" list - something that adds and removes items/units? It'd need some good planning to make sure that we handled it well, but it might be a useful feature (if people don't think I'm too mad!)