Well, it's complicated. While we are entering the war on Ishgard's side, and both Aymeric and House Fortemps are definitely our allies, Middy implies there's a dark secret behind the war. What secret that is, and how people react to it, could easily turn everything on its head. I seriously doubt we'll end up enemies of the state in Ishgard too, so my best theory right now is that Aymeric and House Fortemps might go apostate and we'll end up deposing Archbishop Thordan VII (Ishgard Pope). Nidhogg is definitely going to be antagonistic, though.
I agree, both sides are being played against each other, and ending the war without destroying either side is paramount.
Anyway yeah, Ysayle was pretty clearly just being played by the Ascians. While she has the Echo, Nabriales pretty much tells you outright he taught her the summoning ritual, and it doesn't make sense to summon a Primal if she's wholly on our side. From the look of things we'll reconcile our differences in Heavensward, but I at least want to bop her on the head for being so damn stupid with the whole Shiva affair.