To be fair, PCB may be expensive as a case material, but it's cool as hell.
As the internal antennas are pretty rubbish removing them is lovely. As a side effect you could use lasercut acrylic/plexiglass etc for a cover.
The power switch is very hard to find, try to use a more common one.
Make it a bit fatter so it can easily use the Sparkfun 2000mAh batteries, or 3 AAs.
Upgrade the ATMega88 to a ATMega328 for super-awesome!
As for mainainance, Use Google Code to maintain the source files for uC/PCB?
For ISP connector use an edge-mount pad design, that way there's no need for 2.54mm header pins.
I love the Mini-B idea, I've got a Nokia with the new charger, so that'd suit me perfectly.
I was already redoing the design as a bit of a mental exercise, but instead of that messy 555 I was going to use a pair of DACs to control the VCOs.
I was also looking at this: http://www.hittite.com/products/view.ht ... MC822LP6CE
but it seems like it only covers 3 of the 4 mobile bands, and only those bands with gap in between them.