I prefer the build quality & weight (solid) of the Moto Droid. I also still really prefer a physical keyboard. Otherwise, it's mostly nit-picking. You MAY get updates more frequently on the Moto and the HTC MAY not receive any future Android updates at all. It's foolish to buy any handset in this day & age based on what may or may not come down the line in the future. Out of the box, there's no question the HTC has superior specs. I like the small tweaks HTC has made to the stock Android calendar, dialer, gallery and music apps, for example. They have addressed most of the shortcomings & lack of polish found on the stock Android apps. HTC's camera/camcorder apps & onscreen keyboard are about a zillion times better than the stock ones found on the Nexus One and the Droid, for example.
There are a few other benefits (some unconfirmed) to the Motorola, however. Some reports indicate the Moto has superior reception, voice call quality, and battery life.
One of the only differences I have noticed is that the HTC Incredible sample videos I've seen online look a bit darker and murkier than the Moto's videos (but they are higher resolution). The Incredible's screen blows away the Moto unless you are outdoors in direct sunlight.
If I didn't have either device right now, I'd probably go with the Inc. but I am definitely not going to rush out to sell my current Droid with there are rumors of a Shadow & a Droid 2 at some point in the next 3-6 months.