The truth about Marisa is that she's the ultimate wildcard. The very embodiment of human potential. Where Reimu is stuck in her role as a shrine maiden, Marisa technically can be whatever she wants to be so long as she puts enough effort into it.
If Remilia can actually manipulate fate by pulling its strings into one direction or another, it would have no effect on Marisa - simply because she has no strings to begin with. This means there's nothing to catch her if hse falls all the way to the bottom, but also nothing to prevent her from rising further than regular humans are meant to be.
Yukari - who's in charge of arranging things behind the curtains - probably is keeping a closer eye on her than she does on Reimu because Marisa is the one entity whose actions she can not predict. That one walking freak accident just waiting to happen. That magicians are usually driven by obsession (dolls for Alice, books/knowledge for Patchouli, eternal life and the human-youkai peace for Byakuren) only makes it worse because Marisa's kleptomania and hoarding symptoms ultimately hide a desire for power - namely the power of being on par with Reimu. Hells know what will happen if she turns into a full magician and that obsession becomes stronger than her human side.
In a worst-case scenario, she'll end up like Junko - completely obsessed over a singular goal, and thoroughly unhinged over the means of reaching it.