The way you handle overpowered abilities like time manipulation shows what kind of shounen author you are.
This was a not-bad way of handling it, but really only bare minimum.
Sadly the phasing wasn't handled well at all. The phasing user basically took near to no advantage of the ability and only used it for hiding. Bad hiding even.
That weapon transformation is just an excuse to pull out new stuff whenever it is/will be convenient as seen in this chapter. Her way of getting powers is that trope in general. You can always show a flashback to some training or how she got abilities to validate her way of fighting.