The spirits turn into Ash Wraiths if combat is initiated. Disciples are mentioned as having sacrificed themselves in the Temple to become Ash Wraiths and guard the Temple. Thing is, the Temple was founded thirty years after Andraste died and her followers were scattered. It's possible that the spirits of the dead followers were drawn to the combination of Andraste's Ashes and the one mountain singularity of lyrium weirdness going on, but I think it's more likely that they're Cultists of Andraste playing a role. Maybe. Crap. I think the Guardian is either actually the preserved man, or a spirit of faith imitating him out of respect. I always thought he was Harvard until I got my head out of my ass and realized you talk to 'Harvard' as part of the riddle game.
I'll bet you anything that the volcano that probably took out Barindur was Elgar'nan's sacred mountain.
"GET. OFF. MY. LAWN. *BOOM!*" 
I can totally buy Andraste deliberately martyring herself as a way of not losing the empire they've already built, making their religion solid, and screwing over Tevinter. *snip*
It's totally plausible that these are spirits akin to Cole, as is the cultist theory for the riddle room ghosts; for the Guardian, I'm inclined to believe that there is some hocus pocus keeping at least part of the essence of an original follower alive - he mentions that others were there, too, but they "fell silent." I'm minded of the Avaar statue brothers in Awakening, who basically "slumber" for an eternity despite being trapped there.
I'm thinking - if Andraste was half as clever as I think she was, then her death would have been kind of part of the plan; I could even imagine that after a life full of such burdens dying could even have been something she wanted. The important thing is how. Of course, it could also be true that things really did go down the way that the Chantry taught it (but I really like being skeptical of the status quo opinion).
Anyway, the riddle room ties my brain in a knot because it's too simple and yet too complex - I would by the theory of the spirits of Andraste's disciples being drawn to her resting place, except that all the key figures are accounted for. What are the chances that all those people felt so strongly about this that they would go there upon their deaths? Shartan in particular - according to the scant Dalish lore we hear in Origins, and after the riddle room especially, I got the impression that the elven uprising was more nicely coinciding with Andraste's march rather than the elves becoming devout believers. After all, after Andraste was gone, the elves gravitated back towards rediscovering and rebuilding their own religious roots. So what gives?
SOME WEIRD CRAP IS GOING ON IN THE BRECILIAN RUINS.
The Elder Tree and Zathrian both drop some big hints, as does the Arcane Warrior spirit.
"Who destroyed this place? Was it the humans?"
"No. It was they who built this place, long ago."
I think that's how the AW dialogue went. He remembers fighting something strange, and a lot of imagery that sounded vaguely interesting back in 2009 and is very concerning in 2015. The Elder Tree talks about the Brecilian Forest was tended to by the Arlathan elves, and there was some human and elven mingling. Makes sense. The Neromenian Migration was a long time before the Fall of Arlathan. There was plenty of time for different human cultures to interact with elven civilization in a myriad of ways. But it's still disconcerting. The dwarves are always enigmatic in DA. Cadash Thaig sheltered Arlathan refugees and was exterminated by Kal'Sharok to preserve the alliance, and it appears that there may have been trade contact and occasional violence between the Surface and Underground empires of ancient days.
Arlathan is well-established before the human migration, so I'm willing to believe that this was a colony or independent state of Arlathan. It's part of the Eluvian Network as well.
Yes. Yes indeed. The thing is, I think this is just as cyclical as what I've seen in other similar stories (*cough* Wheel of Time once again prominent among them *cough*), there could have been even several attempts to get the right mesh between elves, humans and dwarves. What is to say that there weren't colossal conflicts between their peoples before? It could even be truly at the root of a whole lot of events that are more "modern," including the fall of the elves and their subjugation, the destruction of various thaigs... I'm still really curious about the primeval thaig and how it connects to all of this. That place doesn't make sense in the context of everything we know about dwarves dating back to right before the First Blight.
Yes. I share the theory that the pantheon was dealing with blight (and probably something to do with them being sealed off).
I think some of you mentioned this earlier -- but why do we think that the old fancy Thaig may predate Arlathan? There are golems and altars of Dumat in the thaig, that's the only reason I wonder. It predates the Memories, to be sure. And on a similar note... with the altars of Dumat in the thaig, and the weird architecture/magical sense, as well as the red lyrium... perhaps there's a connection between blight, blood magic, dwarves, and old gods. Gryphons were once all wiped out thanks to blood magic. Maybe dwarves lost their magic in a horrible experiment too? And if lyrium/red lyrium is what the Profane ate when they say 'feasted on the gods'... and there are altars of Dumat in the thaig... and magic was used in the Thaig... is there a connection there I'm missing?
*snip*
In connection to the previous thought: I think it predates Arlathan because we have at least a spotty idea of who the dwarves were in the past during the blights and a little before maybe, based on the few excavations we know of. If there are human/elven artifacts in dwarven lands, I think that does indicate a connection between the blight, blood magic, dwarves and the Old Gods as you say - it's just that it doesn't make sense in terms of the dwarven context I know (which I'm ready to admit is probably even more limited than that of all the rest of you who have pondered this longer than I).
Also worth noting is that Tevinter had suffered a series of massive civil wars and unrest a few centuries before the Black City incident. Much like Rome, it shrugged it off and kept going. Wicked they may be, I have to admire how ridiculously resilient they proved to be. I think by the Dragon Age, they're equal to Rome in longevity (2000 years, give or take.) Unlike Rome, they managed to remain an empire and retain their homeland at the 2000 point.
(To be fair, if you're going to be reduced to one city from a massive empire, who wouldn't pick the Queen of Cities?)
I think if Andraste or the force behind her had something to do with the Blight, the whole Exalted March was improv after Dumat's death.
There are people more into and with a lot more evidence than I when it comes to the Mythal/Dumat/Andraste theories.
I'm waiting for one of them to drop a lore-bomb on us all. Probably as soon as I run out of likes, knowing my luck. 
Rome.
(I know that was a terribly substantial comment.)
I've been skipping a lot of posts that referenced WOT2 because my copy hadn't arrived and I was avoiding spoilers. What's your alchemy theory?
I'm so glad you asked.
*smug* This is what I wrote on the subject (including the furthering of the elemental theory!):
Yes, yes. In that vein it could even be along the lines of oriental elements: wood and iron coming to mind especially. Added to this spirit would obviously be the connecting force, i.e. the Fade, which connects to all the elements (i.e. peoples) in different ways, explaining the vastly different experience that the races have with the Fade. (I'm still very convinced that the Fade is Tel'aran'rhiod by the way.) Dwarves cannot connect directly, i.e. they do not dream, they are the representation of solid earth; elves have a kind of affinity, which I think is indicated by how they were able to possibly manipulate "Fade-pockets" like the Crossroads between the Eluvians. Humans find it more unnatural to exist in a place like that, yet they do have a connection to the Fade. Also, perception: generally the human viewpoint is dominant now, taking Thedas history into light, which means that the Fade is treated with the same kind of projection-based categorization, i.e. their view on demons being demons. They go in there with solid expectations and the Fade bends to their perceptions, plus they approach it with fear, the concept of "othering." I'd imagine that (taking Solas' hints into consideration) the elves had a very different way of merely approaching such matters, let alone experiencing them. Plus their whole identity is built around "fluidity" you could say. Ok, enough of that, I'll get back to it later.
I'm all in there with alchemy in a broader sense, too (when I was Dungeon Master for Vampire roleplays I would torture players with my alchemy knowledge, MWAHAHAHA): the magnum opus. The four basic stages are nigredo, albedo, citrinitas and rubedo. Translated into Jungian psychology (yes, I know I always end up here) these stages can be applied on a psyche-level transformation by being the Shadow, the animus/anima, the wise old man/woman archetype and the individuation, respectively. Translating this into Thedas as not a process, but a state of being in a cyclical shifting of powers, the Blight/red lyrium is clearly shadow-matter, i.e. the enemy within. The animus/anima is a representation of the purified soul, i.e. we could consider this the Fade in a sense, spirits and essences. The wise old man/woman - well, the first person who comes to mind is Flemmeth, but also Solas (and perhaps other gods); in fact, this could be a representation of the god-sphere in a sense, as citrinitas is the "solar light" which transcends the differentiation of animus/anima. Finally, the merging of the ego and the Self, true individuation in rubedo, the "distilled" product that goes through the previous 3 stages and is transformed.
Yeah, I could theorize on this for ages. I'm probably grasping at straws, though. 
*snip*