A few people have done manual controls for the IMA on the Insight, here. I imagine something would be possible like this on the Civic, though I dont' have the technical expertise to do it myself (beleive me, I would if I knew how...) Given the highly hilly terrain I drive on, and the observed behavior of the IMA, I estimate I could see well over 10% improvement from software changes.

The MIMA system I linked to is not really a hack though, as it's non-destructive, and there's not really any risk of frying your battery or anything either as all the stock safety overrides (such as to prevent overheating) are still intact. What the MIMA circuit for the Insight is emulate the stock signals. When off, the system performs as normal.

The same people as on the above website have also talked about doing not only adaptive software, but predictive controls that could look ahead on the road using a laptop based GPS navigation system (and a USB interface to that MIMA mod), and the software could determine just the right amount of charge and assist to use, knowing what sort of inclines etc. will be coming up.

The fact that Honda did not offer even a slight degree of manual control over the software, such as switch specifying short-trips, long trips, or mountain etc. with different software settings for each is somewhat ridiculous, seeing as it would have cost next to nothing to implement what is essentially just a software change.
yes, I am crazy