There is a lot to consider...
Both are good devices. Yes, the Bolt has some issues right now, but they should be fixed soon and everything should be gravy after that. It really just depends on your preferences.
The iPhone has a lot of things going its way. The display really is top notch, even if the screen is very small compared to the Bolt. The apps you can get are very robust and well rounded and everything is guaranteed to work flawlessly with your device. If a company has a smartphone app, there is a 99.99% chance its in their Apps Market.
The Thunderbolt on the other hand, is great in its own way. The screen is amazing, and even better, its relatively huge for a phone. As far as customization, there is no comparison. Android allows plenty of it, even without rooting/jailbreaking. I have stock and through WidgetLocker and LauncherPro, it looks unlike anything else you will find, and I love it. If you know what you're doing, you can get the Bolt to do far more than the iPhone without rooting. Widgets alone are a selling point, in my opinion. Oh, and if you're in a 4G area, the browsing speeds of the Bolt compared to the iPhone... well, there is no comparison. 4G blows 3G out of the water, but it is a major battery drain, so either you baby the device or just buy the extended battery and not worry about it.
Really, either one you get, you'll be happy, but you'll have a completely different experience on each. Go to the store and play around with each.