Transaction History
Given that an upgrade, or new mod could break existing save games, it would be useful implement a way of rolling back changes so that users can easily revert to a configuration that is known to work. This is not functionality that Portage has (to my knowledge), however the simplicity of this project compared to Portage would make this much easier to implement.
The installed mods database could be turned into a git repository, with some way of determining the changes necessary to update the installed mods to match the new version of the installed mods database. This would give a large amount of flexibility, as we could expose a way for users to set up branches and maintain multiple configurations. Tags/Branches could be used for indicating points to revert to, in addition to rolling back changes one at a time with HEAD~1 etc.