48X24X48X:
You are going to make the power pack separate from the main board right?
Yeah, everything apart from a basic LDO/UVLO is on a small interchangeable daughterboard.
48X24X48X:
While I was working on WSN back then, we usually have this configuration: Buck > Battery Charger > Buck-Boost.
The buck section was meant for the solar panel or some external 12 V SLA battery. The battery charger is for the Li-Ion and the buck-boost to maintain 3.3V. Obviously using this configuration provides more juice of current but the quiescent current is not amazing like sub 10 uA. It was something around 50-100 uA. I haven't really tried on those very low voltage energy harvesting stuff and definitely would like to see the outcome from your side!
Sounds very interesting; I'm very curious to know about your WSN projects. It's something I want to experiment with in this project...when I get time 
But why would your networks have both a SLA and Li-Ion batteries? or is the 12V battery more of a charging station that is not consistently present?
48X24X48X:
I think low power design is challenging from the hardware point of view. But what is lacking is probably a more organized light weight Arduino compatible library without exposing too much of AVR bare metal style of controlling the power (what power state, how long to stay low power, wake up source, what to shutdown, what to stay power on).
Yeah, that will still be the hard part... especially for me as a relative c++/Arduino noob (still digging out of this PIC assembler hole). Help/advice in this area too is appreciated Hard to say where the right balance between performance and usability will be struck - something as simple as providing wrappers for some peripheral functions that will set up the PRR correctly before use, keep track of the current clock divider setting (switch back for timing-critical functions, e.g. Serial.print...) and encourage the user to use the RTC instead of delay loops would probably go a long way for the time being. I have a feeling those who are already familiar with more advanced power managed modes know what they're in for (and probably don't think of Arduino as their first platform choice for such applications...)