As someone who divides his week between the two counties, the difference for me is about which wines each county does best. While there are certainly some great Sonoma Cabs and Merlots, I think Napa is way ahead in terms of quality. Sonoma, on the other hand, beats Napa hands down with Chardonnay and Pinot Noir.
The alcohol debate is interesting. It is driven by many of the same people who 10 years ago were complaining about over-the-top, oaky Chardonnays. In many cases they have a point, but they see it in such black or white, right or wrong terms. It is possible to enjoy both styles; most wine drinkers I know do.
Also, just as winemakers needed time to push the envelope with Chardonnay -- experimenting with levels of oak, barrel fermentation, etc -- winemakers for a while were pushing ripeness in hopes of achieving maximum flavor and aromatics.
I suspect there will always be ripe, alcoholic wines and super-oaky Chardonnays, just as there will always be Chablis-like Chardonnays and elegant, 13.5 alcohol Cabs.
But things seem to be balancing out, IMHO