Thoughts on various combinations and what they might help bring, though of course these are my own thoughts and the author might have some other ideas on the matter. Maybe others have some insights on some other good combos?
[Bane] Reality Glitches
[Boon] Retrocognitive Flashes
With the idea being that reality glitches are linked to the illusionary power in a sense, which would allow one to warp reality itself, most likely a very strong ability in the post disaster world. And Retrocognition might help to better gain insights and understanding of this and how to deal with it as well as any other problems she gets in to. I don't entirely like it though as it falls a bit short on the social and general life front. The two should work well together though, as a fraying reality should give more access to what is actually going on to some one like her, which probably means she might have more ability growth in this path as well as better chances of getting good solutions. So a path to a powerful ability which could have substantial benefits and more good options, but at some personal costs that shouldn't be underestimated either.
[Bane] A mysterious stalker
[Boon] A sister unleashed
This one would probably stack strongly together towards the Dream World, which is related to the collective unconsciousness and relates to things like the Persona, especially as this would probably bias the Stalker to more likely be Persona related. Basically the various things from those games would probably come more in to focus with this. It also gets you more bonding with your younger sister and makes her more competent and less at risk from things like Persona... which might soon be relevant in her life. More knowledge, ability, experience with the collective unconsciousness could be pretty good for Amu, especially as it would probably help boost her skills in various ways while not disturbing her day to day life to much. Potentially something for her to talk about with Utau as well and could get her some connections to certain people and beings.
[Bane] A group of delinquents
[Boon] Symbiotic Bond
This would probably drag Utau closer to her and help offset some of the troubles she gets from the Banes. A fair chance Utau would become a bit more available because her closest friend is now in more trouble and might need some more bailing out, even if it costs her at times in her personal career. That would cause some extra tensions, though unlikely to much as it wouldn't be considered Amu's fault most likely... as they can some what read each others minds. Advantages would be that there would be more mutual skill gain between Utau and Amu from their mutual knowledge in psionics as well as some chance to develop an ability to combine their psionic abilities. Utau probably has a fair bit she could teach Amu still on psionics, so this is certainly something to consider and being closer with her best friend that could with this most likely survive the end, even in pretty bad cases, would give Amu more grounding and mental stability.
[Bane] A prophecy
[Boon] A sister released Dia
This would greatly shift the chance that she personally got the prophecy, as Dia would help her most likely further develop in Precog. This branch would through her flailing 'panic' over the situation probably make her work far more with Dia in improving her precog as a a way to fight against the upcoming end. Due to this she might be given far more opportunities to interrupt things in the ways only a strong precog can, or run in to people she might else never meet.
[Bane] Forced Publicity
[Boon] A connection to the past
These two combined would potentially be able to set off more of a psionics boom worldwide, as it gives the impression that psionics is inheritable and if you are just but in the right family lines you too could be a psionic. Might unearth some of the other psionics families and in general might bring more psionic information in circulation which Amu could learn. The government would probably get in to this as well as other secret orgs that are interested in improving their chances in what is to come, so Amu would probably get extra training and learning chances in this route.
[Bane] A Family Secret Uncovered
[Boon] A key piece of insight
This is most likely the Boon that is not the counterpart of the Family Secret. How ever it may well still be complementary. As in, this might shift any focus of the troubling secret in to improving the insight a bit more and gain a bit more benefit from it. There is some chance this will make family interactions a bit less smooth though, so there is a substantial social and general life impact risk from the Bane. Over all impact from this is kind of unclear though, so it's a bit of a gamble, Family Secret in general is a bit of a risk really.