BA: What are the disadvantages to these powers?

I think you're over-reacting to the possibility of Mary-Sue-ism. Just because a character has a special power does not mean they need a downside to that power. What makes a Mary-Sue is someone with a power that trumps all others and they can use it whenever it is needed, however much it is needed, to do whatever they need. For most of these powers, nothing more is needed than a limit--a limit as to what one can do with the power or how often they can use the power. A common downside to powers is some sort of weakened state for a time after using the power, or it may harm the user if overused--thinking of good ways to use those two concepts is always a good idea.