I agree.
After looking over Mikoto's abilities, it seems like she has the upper hand in terms of versatility, intelligence, and range. Her range is crucial here.
John is very adept at CQC. In the beginning of the series, he was consistently shown capable of battling powered foes with nothing more than martial ability and wit. Mikoto typically relies on her powers to attack from a distance, and as such would be embarrassed in CQC if John were allowed to get close.
Misaka being in one shot territory actually makes Hunter pointless, as she's one shot by anything regardless. And while John does improve upon the abilities he receives, it's NLF to assume that he could use the abilities to the extent that Misaka uses hers. John typically comes up with only one to two new applications of the ability Such as using Arlo's barrier to surround opponents to prevent them from attacking, or using Blyke's lasers as a form of danmaku by firing them from his fingers. Whereas Misaka has dozens of applications for her one ability to generate electricity.
It seems likely that Misaka will play the range game since John likes to get in close. Phase shift makes it so he'll gain a speed advantage each time he uses it, and Blyke's lasers give him more maneuverability. Additionally, he can actually cancel out her electric attacks with his own, such as what he did to
Remi. Which will make it all the more difficult for Misaka to keep him out.
However, the main advantages that Misaka has in her favor are her superior range and intellect. As well as the fact that she has multiple attacks that can one shot him. Between her railgun, iron sand, and lightning strikes. Generally speaking, John's attacks don't tend to surpass more than perhaps two dozen or so meters. Whereas Iron Sand, lightning strikes, and railgun all have better range than that. Additionally, Misaka can slow him down with her iron sand, mitigating the speed advantage entirely. Lastly, her higher intelligence means she'll be coming up with more effective strategies to use against John than John will use against her.
I think the battle is rather close, since John has multiple tools to get in close in the form of phase shift, cancelling out her electric attacks, and energy beam. But Misaka's options are a bit more effective since she can block him with large walls of iron sand that are impossible for John to break through, take away his speed advantage, and one shot him with multiple techniques that have better range than any of his, barring energy beam. Once she gets out of the early phase of the fight, where John will likely attempt to close the distance with a burst of speed, she should be able to handle it from there with her superior intelligence. It won't be easy since John can cancel out her electric attacks, but since she has options besides just pure electricity, in particular her iron sand, she should be plenty able to hold out against John's onslaught enough to get one of her one shot worthy attacks in.