I think in a story like this (or any piece of fiction for that matter), there's always room for interpretation. Those twins might have been apparitions or actual girls. What are they exactly? The answer is up to you. How did Bandou get a functioning body again? Your guess is as good as mine.
Lucy had to die, even though we all wanted her to live with the Nyuu personality. She accepted the consequences of her actions as a rampant dichronius, and I think it's a fitting end. The props should be given to Nana, who truly avoided Lucy's fate.
I believe the author exercised the fact that Kouta was the only person that truly mattered to the true Lucy in her unfortunate life, hence the twins appearing after Kouta opened the note. It was a very touching gesture, along with the resolution of the plot. Sure, everything went back to normal so quickly, but what else could you expect? As a writer and aspiring amateur mangaka for my own pleasure, I would end my story just around the same.
A riveting tale told in blood and intense emotions leading to a melancholy conclusion -- a true masterpiece to those who choose to appreciate it.