Hypertuned/Resonant

[Enkidoh]

My current hypothesis is that Krile was captured and used to create the Resonant by extracting bits of her soul and transfusing them into whoever they wanted to achieve Resonance. There has to be some specific reason they went after Krile and held her where and as long as they did. This does invalidate the "Hypertuned are just failed Resonants" hypothesis, but I'm fine with that.

I think it was simply pragmatism - 1.0 made it clear most people awoken to the Echo actually hide their powers fearing persecution from ignorant people (not entirely unjustified either as it turns out), which is why Minfilia set up the Path of the Twelve before the Calamity to provide a sanctuary from persecution for those with the Echo and to research it's powers (so as to better educate Eorzeans). Most of the Path's members were sadly lost in the Calamity or not long thereafter (as a significant number were adventurers), which is why Minfilia reorganized it into the Scions of the Seventh Dawn.

Apart from Minfilia, the only known Scion after the Calamity to have the Echo until Krile was introduced was the player/Warrior of Light, everyone else in the Scions were either just random adventurers who joined after inspired by their success or the Archons (unless you count Una Tayuun and her friends Percevains and Satzfloh who were originally in the Path of the Twelve before the Calamity and rejoined after as Scions suffering amnesia, only to be killed sadly ironically during Livia's attack on the Waking Sands).

And given Minfilia's... ascension... and the Warrior of Light is a very hard man/woman to find at the best of times given our transient nature (and Zenos was more interested in us being a challenger to fight rather than a test subject anyway), it left the Empire with only one remaining possible known Echo user subject that they could easily capture: Krile (which is somewhat ironic given Krile's Echo ability is rather low).

So basically the Empire used Krile as their Echo power lab rat simply as they had no one else, it was pure pragmatism. Of course that doesn't make it any less horrible though.