Yea, Kurata and D-reaper should be higher. Ken does deserve to be in the top but not as high as he is. Vamdemon most certainly #1. He left the biggest impact on the series as a whole. I wouldn't be surprised if he pops up in Tri as well.
Apoclymon literally felt like a tacked on final boss. He came out of nowhere and ended up failing everything. So much injustice to that one in the series.
Blackwargreymon and Beelzebumon I always considered to be antiheroes more than villains. I don't think either should be there.
And Iggdrasil not being there is a sin.