Batteries, howto make a board that can run a year?

I would omit the crystal. This gives two additional IO pins and reduces power consumption. Instead I would add some quality RTC. This would allow for superior timing. It also would allow to go for deeper sleep modes thus resulting in even less power consuption.

If exact timing is needed the AVR RC oscillator can be calibrated. Since the RTC solution provides a reasonable good reference it is possible to recalibrate anytime exact timing is needed.