It doesn't have to be this way. When I upgraded my Air from SL to Lion last year, it was the most painless Major Change in 5 years. Under 1 hour tops, including download time and testing some 50 apps.
Not an appropriate comparison. The number of iOS devices updating today far exceeds the number of Lion Upgrades done, probably to date, by 10 fold.
I'd guess that this is probably the largest, most involved software update Apple has done on a single day (Lion, iOS across all devices, and iCloud setup or migration) and expecting it to run smoothly is being overly optimistic. That being said, I'll agree that today has been frustrating to say the least. I spent a good 3-4 hours trying to get my iPhone updated this afternoon/evening but things appear to have calmed down a bit as I was able to update my iPad 2 on the first try and even my Apple TV updates appear to be going smoothly as I type this. Patience is a virtue on days like these. Heck, if all of us (myself included) weren't so damn eager to get the latest and greatest the second it's made available, this probably would go a whole lot smoother. Regardless, still a hell of a lot better than the Android update ecosystem.