Any reason you can't just sleep/suspend your system at ignition-off? I can see that there might be times when the system does go down hard and you've got no option but to reboot, but still, that should be rare.
I work with a fair number of embedded systems myself. Most avoid full boots where possible.
Depending on the app, sleep may be possible. But for some apps, like automotive, it is not surprising to see requirements like current draw being less than one milliamp in the sleep state.
I haven't seen or heard of any embedded apps which hibernate to flash. That would not be terribly fast, and would wear out the flash quickly.
That could raise some interesting engineering/maintenance considerations.
A local capacitor might provide the latent power to support sleep state. Or you could provision flash with enough ECC and reserve capacity (a 16 GB microSD drive fits on my pinkie nail) to survive years. Might even make swapping the storage a regular maintenance item, say 5-year cycle. Figure a high-end duty-cycle of 10 starts/day, 365 days/year -- that's 3650 read/write cycles a year. Even if that's a 100x low estimate, we're talking 365,000 cycles/year (that's assuming 1000 starts/day). As of 2003, AMD were discussing 1,000,000 cycle lifetimes for flash storage: http://www.spansion.com/Support/Application%20Notes/AMD%20DL...
Actually, in five years, controller technology would likely advance enough that, provided your unit production count is high enough, you'd just swap the entire controller for a new component with enhanced capabilities.
I work with a fair number of embedded systems myself. Most avoid full boots where possible.