@InfiniteVerisimilitude First, a correction, general esper levels indeed have to do with power, going from able to bend a spoon all the way to be able to fight armies single handledly. What I meant is that
Level 5 rankings are the ones that have nothing, or at least little, to do with how powerful you are.
To answer your question, Level 5 rankings are based on the importance of the Level 5 in question on the research of achieving SYSTEM/Level 6, that is reaching the level of a god while in a human body, the ultimate goal of Academy City. So even if Mikoto got "power gains" (which I really doubt she did in the first place), if it doesn't help further the plan, she stays as #3.
This is mentionned by Mugino in chapter 30: