One thing that's not covered in the anime probaly because of time constraints, but in the manga was the fact that Rido was just a
tool being used by the counsel to further their agenda. He was going to be more like their puppet. He was never a major adversary other than the fact that he did some really evil things, wanted yuki and his existence bounded kanames powers. The plot leading up to the battle or that takes place along side is much bigger in the manga and never appears in the anime. For example kaname never appears in the rido, battle because he was off somewhere else in a battle of his own. But he does come at the end of the battle thanks zero for killing rido and then zero and kaname have a battle of their own -
over yuki. This could never appear in the anime without makeing a season 3(which they don't have enough material for)
so the ending was perfect
As far as kaname and shizuka. They animated the shizuka part in the anime exactly the way it appears in the manga which might be why it seems more complete. However with respect to the anime kanames plans didn't all go accordingly.