1x Tex*2 > 2x Tex*2 = 1x Tex*2w/Alpha Non *2 textures are totally fine on hardware that is not mobile based, basically anything that has the same power of that the PS2 shouldn't be using non*2 textures, although they used plenty of rectangular textures in FF series.
less texture calls with the rectangle, and if your using it for a unwraped model, possible less UV splits since you can have longer islands and still maintain proper scale. for a unwrapped mesh i would go rectangle, if your speaking of tileing textures and trim sheets i would go 2 textures.