Ah, I like this. Hoenn and I have a very strange relationship - it would perhaps be most accurate to say we've been through a lot together, not all of it good - and whenever it turns up, I always greet it like an old friend. Then again, I greet many inanimate/imaginary objects like old friends, so I wouldn't read too much into this.
Before I get to the meat of this review, I have to cordially disagree with psyanic on two points. Firstly, his assertion that in this bit:
you could replace the full stop/brackets combination with a comma. This would create a comma splice, which is one of those grammatically-incorrect things that only established writers seem to be allowed to use; however, if you use a semicolon rather than the comma, it would be perfectly legitimate. Secondly, psyanic denies that 'ponderings' can be considered a word, since it's a verb; I would argue that it's some sort of gerundive noun, if such a thing exists, and that you're well within your rights to use it. Sure, it may not strictly speaking exist, but it fits with Virgil's tone - cynical and mature, but with hints of youthful slang breaking through here and there.
Anyway, that's just my opinion on that; make of it what you will. On to the story.
I really, really liked it. The Hoenn story has tremendous potential as fodder for adaptation, because it isn't as detailed as the Sinnoh or Unovan stories, and it isn't as vague as the Kanto or Johto ones: in short, it gives you just enough freedom to subvert it a lot without it departing too far from the original. So, as a fellow Emerald-storyline-based-fic author, I commend you on your choice of starting point. It was a sound one.
Furthermore, as has been pointed out, the cynicism is fantastic here: it's not the frankly cloying angst of most dark stories out there; it's not the bland happiness of the more traditional sort; and it's not the mild (or in some cases extreme) lunacy typical of some of the comedies. It's novel and refreshing, and in a canon flooded with generic stories, that's probably one of the most welcome things that I can think of.
Actually, I remember experimenting with a cynical story last year or something, but that was actually a comedy disguised as a noir detective tale, so it doesn't really compare to this.
Where was I? Oh yeah, the cynicism. Yes, that's all good. Moving on, let's discuss the people.
Virgil's a funny kid, I think. I'm very curious to see what's up with his face - that's good narrative technique by the way, hinting at something wrong with it like that - and his mysterious past only sweetens the deal. (Oh my God, referencing things seems to have become pathological with me. I'm so sorry.) The other people of Littleroot intrigue me, too: their limbs swathed in bandages despite the fact that their wounds all heal immediately, their curious apathy, their strange predilection for forming random families... yes, there is a great sense of menace built up there in the details. It's the classic subverted idyll scenario: we are presented with what seems like Arcadia, but it's pockmarked with tiny defects and flaws that, because everything else is so perfect, are deeply, deeply disturbing.
I do have one minor complaint: I would agree with psyanic that you should remove the spoiler tags; they're not necessary and are prone to malfunctioning so that they won't open.
Briefly touching on the whole Divine Comedy thing, I'm not certain I particularly see any parallels between this Virgil and that one, other than the fact that both are surrounded by trees at the beginning. I'd be more inclined to believe that Virgil's just named after the real Virgil, a fictionalised version of whom is Dante's guide through the afterlife in the Comedy. Alternatively, there might be no link at all and you just like the name 'Virgil' - and why not? It's a good, hearty Roman name, and you can't say fairer than that.
To conclude: I enjoyed this very much. It's well-written and a pleasure to read; though I say this at the end of almost every review I write, you can be sure that I really do mean it when I say I eagerly await future chapters.