So after the water temple, the guides say you must head for the shadow temple. Yet the game itself directs you to the Gerudo Valley and Fortress (Blinking locations on the map) after completing the water temple. Also in the status menu the spirit medallion comes after the water medallion. You don't need the hover boots for the spirit temple and you obviously don't need the mirror shield and silver gauntlets for the shadow temple. You aren't even given a hint about the shadow temple. So how come the guides point you for the shadow temple before the spirit temple if, according to the game this is where you should be heading?
I think the guide says the Shadow temple first because you need the Lens of Truth for both the Shadow and Spirit temples, but since getting it is linked to the Shadow temple (shadow monster coming out of the well, etc) then it makes logical sense to go there first. Besides, you're right there, might as well do it.
I will say, I've never understood why they put the Spirit song and such before the shadow song on your subscreen when they clearly mean for you to go to the Shadow temple first.