The flexibility with the battery provision is great - let people choose what they want.  The reset link for the super cap a good and necessary feature.

Minor gripe / observation is the connector for the remote battery pack and the lack of keying it for polarisation.  I know the board is screened to indicate polarity, but I'd like to see some fool proof way of getting it right way around. There are plenty of us fools out here.  Maybe the circuit provides reverse polarity protection?  I'm not familiar with it and if so  then all good.

In any case I reckon you are doing a great job.