Droid:
-Keyboard (some games require a keyboard)
-Battery life
-Huge hacking community
-Root abilties (tether, under/overclock, themeing, etc
-Stock Android if you don't like Sense.
Incredible:
-Sense UI
-Better Camera
-Faster processor (if you don't plan on overclocking your Droid)
-Lighter (But plastic)
-Optical trackball if you like that
Really, in MY opinion, only go with the Incredible if you want Sense UI, or if your phone will be your camera.
Actually, I have to say the opposite. The Inc is a better phone all the way around. Root ability will come with time (kinda silly to use it in a comparison IMO) and you haven't even listed half of the improvements over the moto droid. Looking at the two side by side and using them, there is no contest. If you like to go by specs it's not even close.
I would have to say that the only reason to even look at the moto droid is the physical keyboard, which is going the way of the 8 track tape, or to feel a bit of nostalgia for a phone that USED to be the flagship device for VZW.
People that hang on to this moto droid as a competitor in today's market are probably listening to cassette tapes on their walkman and arguing with their friends how dvds are as good as blu rays. Give it up, it's old tech now, as the Inc will be soon. That's why the new droid will be out soon, the entire market has changed since the relic, errr moto droid came out, and it's time for them to catch up.
Also, the moto droid may really get put down for the count when the shadow comes out if the rumored specs are indeed true. I will admit though that my moto droid I have for work is untouchable in the always important paper weight category.