What if Reimu became Yukari's shikigami?
I think that'd be a natural choice for both of them, given that, like you said, there's a not-too-subtle plot the Moriya shine is hatching to try and rival the Hakurei Shrine in terms of Gensokyo's seat of power. I think the struggle between the two is not just political but spiritual. Comparing the shrine maidens of each, Sanae is a modern girl newly arrived to Gensokyo, while Reimu - having lived her life in Gensokyo - represents a more old-fashioned mentality.
Things have taken a detour from this conflict, though, as the spiritual composite of Gensokyo becomes more mixed, thanks to common enemies. In UFO and Ten Desires, shrine maidens from both are investigating interlopers bringing new spiritual faiths into Gensokyo. The Hakurei Shrine and the Moriya Shrine both have a vested interest in getting the better of the newcomers while leaving their opponents at a disadvantage.
I think if the Hakurei Shrine and its allies mean to survive, the major players there will have to put aside their differences, swallow their pride, and form a concerted effort to retain control of Gensokyo. That would include, I think, Reimu agreeing to let herself become a channel for Yukari - a whole new united front. It's getting pretty medieval up in Gensokyo.
What if the person buried under the cherry tree was Youmu?
