What I think would be neat would be to provide the ability to write scripts to help solve. Since the game is written in Flash, it would make sense that the scripts would be written in ActionScript which is very similar to JavaScript. There would be some macro type scripts that non-programmers could use to eliminate some of the drudgery involved when you first start out making strings (after they run the script they can continue solving as before).
For people comfortable with programming you could provide functions like targetPairing(myBase) which would return the identifier of the base that is supposed to be paired with myBase. There would be properties too like myBase.type might be set to G, for example. This would allow a programmer to write conditionals and loops in the context of the game environment.
What I think is cool about this idea is that if done well it could be helpful for most intermediate/advanced users or any user that realizes that there is often a consistent system. But it could also draw in others into Informatics, even those that wouldn’t otherwise be inclined to do so.