In response to your points:
1) Nobody was saying the D3 is a "large" phone. The issue about size was strictly in comparison to the Inc2. There is no question that the D3 is a bigger phone than then Inc3. So, if thin and light is your top priority. the Inc3 is the better choice.
That said, I don't know how anybody could objectively claim the D3 is not chunky. Outside the monster phones with 4G and 4.3 inch screens, it is certainly one of the largest phones on the market. Its about as long as the 4.3 inch Thunderbolt and probably thicker than any other phone in VZW's lineup (and, no, I have not checked so this is just a guess). I think the size is very manageable and well-worth the trade off for the large screen and super keyboard. But, it is large - like many of today's flagship Android OS phones.
2) No offense, but I honestly don't know how anybody can objectively claim the Inc2 has an inferior screen to the D3. Side by side, its not even close. Of course, you are entitled to your opinion. But, I'm pretty certain that no objective tester would agree with you.
In a way though, it is a moot point. The OP is choosing between the D3 and the Inc2, and like most others, he personally prefers the screen on the Inc2. So, the plus is in the HTC column for him.
3) On paper, the dual core processor should be a big advantage for the Droid 3. Practically, the Inc2 feels a bit more responsive than the D3. This may have to do with Sense being more snappy overall than Blur (or whatever Moto is calling their skin these days). However, I believe that the typical non-power users won't even recognize that the D3 has a more advanced processor.
I'd still choose the D3 over the Inc3, because of the wonderful keyboard. Still, if we want to be objective, there are pluses and minuses to both units.