i actually bet he had the master at least tentatively planned from the pretty near the beginning - "daleks for s1, some other overarching villain for s2, and the master for s3, if we get it!" the master is the kind of villain you'd plan to bring back, because he's so well-known, but not right away, because they'd done the daleks already, and weren't quite sure how the public were going to be about bringing back old characters/monsters. if the public hadn't liked that stuff i'm sure he would have scrapped the master and done something different. also, he definitely had the toclafane (name and everything) planned out as the bad guy monsters for the s3 finale when they were still writing s1 (you may have heard about how they lost the rights to the daleks at one point, and shearman had to compleetly re-write dalek with the toclafane instead. and then rewrite it again when they got the rights back). so i think it's possible he had a vague idea of how the doctor would find the master at the end of the universe and bring these spheres back with him to take over the earth.

so later, when he was actually writing it, he might have been, how can i tie this in more... haha, i have it.

As for the themes, though, hasn't he said something about Ten's massive hubris, that his good intentions always go south?

that would be interesting if he had. i don't know.