I took Nova's side because Horner and Raynor said it themselves: «if we're to win this revolution, we've got to be sure of our allies», and I was kind of suspicious of Tosh. Turns out Ghosts lose their EMP usefulness because there's only one versus-Protoss mission left, "Supernova" -- in "Maw of the Void", the disintegration "aura" makes it a bad idea to use Ghosts.
Ghosts might be nice versus Zerglings and Marines when using that range upgrade, but Spectres can deal with them equally well because of their AoE stun + damage (Psionic Lash Ultrasonic Pulse), I think it even stuns Ultralisks although they should, supposedly, be immune to it. On top of that, they deal bonus damage versus Armored, which is welcome to quickly kill Overseers.
I ended up going for Spectres when I played the campaign a second time.