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^This. See Castrum Occidens in Eastern La Nosca where the XIVth Legion managed to get to one of Dalamud's fragments before the Eorzean Alliance did and built a research center on top of it. Ironically... the WoL cleared out most of the fragments defenses that were keeping legion out...
The Empire also purposely destroyed a lot of the places of worship to Rhalgr found throughout the Peaks as they banned religion when they took over Gyr Abania. So that's also a major reason why there's so many ruins around.
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The Garlean Empire only merely continued a policy of destruction against symbols of Rhalgr started by Ala Mhigo's Mad King Theodoric though - when he proscribed the Fists of Rhalgr he virtually purged everything associated with the worship of the God of Destruction, regardless of whether it was part of the Order of the Fist or merely a religious centre, declaring only worship of Nymeia the Spinner to be Ala Mhigo's official state religion.
Hence the various ruins in the Fringes and especially the 'Destroyer' statue at Loch Seld were specifically destroyed by Ala Mhigans under order from Theodoric, he even turned the Divine Audience stairway that was an altar for religious ceremonies for the later statue into a place of execution (this is why the statue's head is sunken to the bottom of the Loch - Theodoric ordered his soldiers to send it to the bottom to get rid of it).
The Garleans, being atheists, merely continued this policy, although it was part of their "no religion allowed" mentality which they placed on all their conquered states. Incidentally, as far as the opposite 'Ruiner' statue also being destroyed, which is clearly a statue of Theodoric himself, well, it's likely that was destroyed by Ala Mhigan citizens in turn, wrecking their vengeance on the most visible symbol of the King of Ruin after he had been deposed, somewhat ironic when you think about it. :p
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The sightseeing log for 'Southwatch' in The Lochs paints a picture of some places simply falling into disrepair due to lack of use.