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@ Blood Liberal - Yes, but Last Exile and Trinity blood had the same aspect to them. They both skipped at the crucial part to get it over and done with, and left you guessing what's gonna happen next.
Last Exile skipped right where Exile had shed its Cocoon, Trinity Blood stopped right when Abel was attacking his worst enemy, and then they went to the epilogue.
@ Exiled Poet - So then it works just like Eureka seveN then.
There is supposed to be a picture of them all in the epilogue, with Dio's waving hand and foot coming into the picture as they smile at him, which is actual art by the Manga Artist and not fan-made.
I actually didn't mind Dio, since he was kind of the whole "Anti" which made Claus and Lavie try harder. I thought he had a good development, and the sad part is he never learned Claus's name (which is why he was probably so happy in the Grand Stream, cause he would get to learn "Immelmann's" true name), however, he thinks he himself killed Luciola.
However, it is also a mystery of why his voice is heard on the Silvana yelling ascending, taking to note he could've simply snuck on or he could've fell and got into the Engine room after Exile "erased" the Grand Stream.
...Looking forward to Clannad episode 4 xP
I'm absolutely certain Dio knew Claus's name. Not only had he heard it being said a crap load of times throughout the series but he actually called Claus, 'Claus' once, when they both returned to the abandoned Silvana.
On a side note: I'm sure most are already aware, but it seems that Murata has been quoted on saying that Dio was picked up by a guild ship after falling from his vanship, as written in a certain book or some such thing.
I also do not think him being alive would ruin the ending in anyway, as he would still think he was the cause of Luciola's death, until 'enlightened', which may be not be simple considering his broken state of mind.