I agree that I would have preferred Scry to be part of Spellcraft. I really like skills that have more uses and are not too limited, and Scry is possibly the worst example, because you can even take it before being able to use it at all with a spell or device, and often you may be even compelled to take it immediately to be able to max it out.
Another example is Intuit Direction: a limited-use and trained only skill that could have made sense to be part of Survival, if the other skill was not specifically aimed at "Wilderness" (you don't need ID really in the wilderness if you can see the sun, the stars or the humid side of the trees - you really need ID only if you're lost in a dungeon).
IMHO, while I can see a reason for ID to be separate from WL, even if it make one of the least wanted skill, I really don't see a reason why Scry wasn't part of Spellcraft in the first place. It would be exactly the same if there was a skill called Summon used only for checks done in summoning spells, which are few. Maybe they wanted an extra cost for the scrying spells?
Unfortunately, I think it's quite late to change it without consequences.