I am not sure as to what the difference truly is, but here is my reasoning for getting the 1000:
I have had 700 and 750 cc bikes, even one 550. The 550, even though it was modified for more HP, didn't have the kick I wanted. Since there is only 100 cc difference between that and the DL650, I had concerns.
The other big concern I had was that the 550, 750, and 700 were way too light under my a$$. It was like riding a BMX bike at really high speeds. I wanted the extra weight under me, although 458 lbs for the 1000 is only 31 lbs heavier than the 650 it is still 31 lbs of vehicle weight. I am not sure how much the Givi bags and trunk weigh, but that adds some there as well. Considering that it is still lighter than the 624 lbs that my other bike hefts around I wanted as similar as possible since I had concerns from other bikes I have owned.
At any rate, I am sure that there might not be any real difference for the average person and that they don't (probably) think in the same fashion as I do, but I am 6'4" tall and weigh 280 lbs. I am not able to ride some bikes just due to my physical size and vehicle needs. Even when I had the smaller bikes I was at 200 - 220 lbs. That might make a difference, maybe not. At any rate, personal preference for me was that bigger engine with more weight.