Actually, who didn't subvert it? Only name that springs to mind is Penelo, but she doesn't get enough lines to be it and what lines she gets makes her come off more like the responsible big sister archetype and long-suffering girlfriend anyway. I can't really think of anybody in IX or VI who fits either and can't remember IV and V well enough to tell. Seems like they just take a spin on it every time. I'd still say that Aeris doesn't really fit at all and with Vanille it is a deliberate deception rather than just taking a spin on it.
Paine comes off more like the dark but safe member of an idol group. Lightning on the other hand has serious issues, even during flashbacks, and her overcoming them is probably the biggest subplot in the entire game. There is also the maternal side and the sense of responsibility in her mundane life which are important to who she is, even if she's not exactly great at expressing them. They share the badass, obviously, but beyond that I'd say that what they're going for is substantially different. Also she doesn't angst, whenever things gets too much for her she acts whether her plans are a good idea or not, which is a pretty big departure from the broody, flanderized version of Cloud. And again, having internal issues she's wrestling with and which are clearly shown as flaws rather than something to make her come off attractive and fixable is different, than just being vaguely angsty. Vengeance isn't exactly a major motivation either.I admit I could have been clearer here. While Square has referred to Lightning as Female Cloud, I think they refer to AdventChildren!Cloud or KingdomHearts!Cloud. Basically, Cloud after they watered down all of his traits to a simplified version of his endgame self, which resembles Lightning far more than pre-reveal Cloud. And I was actually referring to Paine there (a FF X-2 man character), despite my sarcasm.