I'm not even sure why I'm writing this all... Perhaps I just wanted someone's opinion about the way I nerfed Reimu. Is nerfing really necessary? Or is there some other way around it, while still making things interesting?
"Nerfing" Reimu by directly weakening her powers might be a little tricky; some fans (though not all fans) might get upset if you tweak canon in a haphazard fashion. That said, if you do it right and do it in a way that makes sense, you probably won't piss too many people off.
Some potential explanations for why Reimu got nerfed:
It turns out that Reimu draws her power from an external source (the Gensokyo border, the god(s) of Hakurei shrine, her yin-yang orbs, etc.), and that external source was destroyed or weakened in some way.
The Hakurei god(s) finally got fed up with her chronic impiety and cursed her.
Yukari warped the border between "floating" and "not-floating".
Eirin's shady new drug Does anyone think that trying to stick to canon in fanfiction is a fool's quest? Please, let me know.
Derivative works--whether it be film, or fiction writing, or comics, or what have you--must always play a balancing game. One one hand, you have adherence to canon; on the other hand, you have deviations from canon.
If you adhere too closely to canon, then the question becomes: why I am I reading/watching this when I could basically just read/watch the original thing again? If there's so little difference between what you're making and the work it's deriving from, why are you creating it in the first place?
If you deviate too much from canon, then the question becomes: why are you even associating your work with the thing you're supposedly deriving from? Why call it a Touhou fic at all?
So depending on your definition of "sticking to canon"--yes, sticking to canon can be a fool's errand. People have certain expectations when they read derivative works, since they typically come to experience derivative works after having read or watched the thing it's deriving from first. In their mind, Reimu behaves like ___, Marisa looks like ____, danmaku battles work like ____, and so forth. Play with those expectations too much, and people start getting too distracted by questions like, "Wait, is this really Reimu?" or, " Hey, the Reimu I know doesn't act like that!" This does not mean, however, that you're forbidden from telling stories that play with those expectations somehow.
I suppose what's more important that sticking to canon is having a good understanding of it, and from there crafting stories that fit a particular vision or interpretation of the canon (or perhaps the opposite: take up an interpretation that fits with a particular story that you want to tell).