I guess this forum is pretty quiet these days, but I thought I'd stick my oar in anyway. First of, I really liked Simoun. It's certainly one of my favorite TV anime series. I thought I'd mention that, because I'm about to be critical of some aspects of it.
I thought that what Simoun did well it did very well. I also thought that it was quite flawed in some ways. I like it a lot because I appreciate what it did well, but I am not quite as quick to let it off the hook for its failings as some people (though I do think it is one of the best anime series I've seen even given those failings). It's fine to say that it's primarily about the characters, but it promises to be about other things as well, and it breaks some of its promises. The only conclusion I can come to is that they were pressed for time and/or money, and that there was poor communication between the writers about some things. I can't help feeling that they wrote the show as they produced the episodes, and that they changed their mind a few times. I'd also be surprised if there weren't some serious disagreements between the writers that never got resolved.
Spoiler:
I don't necessarily require definitive answers, but I like to think that the writers at least know what happened. I don't get that feeling from this show, and the Dominura/Onashia thing, along with the ambiguity over timelines and the timing/membership of Chor Dextra are good examples of this. I agree with WanderingKnight that there are just too many hints dropped about this for it to be accidental- the writers had to have meant to imply that Dominura was Onashia in some places. If Dominura isn't Onashia it is a strike against the writing, IMHO, for having dropped all those hints. The kicker on this one is Yun's line after Onashia's disappearance.
The problem is that the show also gives us a lot of reasons to think Dominura isn't Onashia. In particular it seems like they just weren't on the same page about when Chor Dextra started, how long it was around, and who was in it. I also have the strong feeling that they meant to have a twist involving Aeru's grandfather, but wound up abandoning it.
There's a lot of other stuff like this in Simoun. It has been praised for its world-building, but I had the strong sense that they hadn't really thought the world out very well. I can't come up with any view of the world that makes sense and is consistent with the series.
Also, they seem confused about when and where Dominura and Limone end up- the origin of the word Aeru is important here, and it's hard to make things add up.
I don't agree with yononaka that you have to rationalize to think that the series is very good. By the standards by which I judge anime it is an amazing series, IMHO. But I do think you have to engage in absolute contortions to think that they didn't completely drop the ball on the riddle-like aspects of the show. I think Simoun would have been even better if they had been able to take the time to make it at least coherent.
Anyway, that's my answer to the Dominashia quandary... there is no answer because the writers weren't all on the same page about it. I do prefer the Dominashia answer though
. The hints are just too strong to ignore, IMHO. Unfortunately you have to retcon the series to hell and back to make that make sense.
EDIT: ANyway, after having criticized the series I should also praise it, as I really did like it a lot. My favorite part, by far, was the end of episode 8. I think that has to be on of my favorite sequences in all the anime I've seen. Not quite up there with the Mugen drowning scene in Champloo, but not far behind. That line of Neviriru's "tachinasai..." is just so great, and it's delivered so well. I care a lot about the voice performances and both Neviriru and Aeru were really well voiced, particularly in this scene.
On a kind of geeky note, that line of Neviriru's really reminded me of Ochoufujin (Ryuzaki Reika) in the live action "Ace wo Nerae". She's a very similar character in some respects, and her speech patterns are similar too. Though they will never do it, if they made a live action Simoun the actrees who played Ochoufujin (Matsumoto Rio) would not be a bad choice for Neviriru. She doesn't look much like her, but who does? Ueto Aya from the same series has the physical look for Aeru, but unfortunately I don't think she'd be able to carry Aeru off.