Except the PRT was largely the same when I wrote stories from Aegis' perspective (early on), and from Armsmaster's perspective, or Miss Militia's (then called 'Assault', and a little more reckless, but I digress).I think part of the problem with the PRT vs Undies argument is the nature of the story itself. Skitter needs a reason to be a bad guy. It wasn't her original choice it isn't her natural inclination. By putting the reader in her head the author pretty much has to justify the decision to be a villain, hence the Undies have to be cool and the PRT have to be assholes. To a degree he/she does this by always making those they are fighting worse than the Undies themselves, so the reader gets to chose the lesser of two evils.
Without getting too Doylist about it the PRT exists the way that it does to prevent Skitter becoming a hero despite her own inclinations. I don't see a problem with that being part of the narrative.
The setting was cobbled together from a hundred different short snippets I wrote. The reason I gravitated towards Taylor was largely because she had the ability to interact with many of the key setting elements from the outset. She came after the rest of the setting did, almost.
Up until the day I wrote Shadow Stalker's interlude (Sentinel arc), I hadn't decided on Taylor going full-on villain. I came darn close to flipping a coin, as far as deciding to have her return to the Undersiders (I'm kidding - it was rooted in story events, but I debated it heavily), with the alternative being Taylor striking out on her own as a hero and eventually finding her way to compromise with the heroes and trying to struggle against the screwed up system, (with a tertiary relationship to the Undersiders and other local villains in the midst of the S9 event, which I was still considering at that point).