Some of the arguments about power and skill are too simple, there are a number of factors, power and skill just stand out because they are things we the audience can visually measure, but there could be all sorts of factors that Weird will decide matter or matter more, some powers are just better, some powers are a bad match up for another, for instance even if the MC reached level 4, if he doesn't get a handle on handling electric, a level 3 Met would wipe the floor with him. Nico is going to dominate someone who could be completely immortal and have near limitless strength but struggle with someone who is very agile. Then there could be unknown factors, that we are still only guessing at, how much does the MC's regeneration place him above the average person of his power level, how much does Alice's destructive power?
Then of absolute critical importance, the power of plot, things need to happen for the plot to continue, and some of these power levels could just be pulled out of the authors ass.
For us the readers, Cole had more power, the MC made up the difference by fighting with smarts, and you could also say, a powerset that wasn't completely at the Mercy of Cole's, so it works within the story that he can beat Cole.