The author completely dropped everything having to do with that senpai he had a crush on at Tokyo U
She's not a senpai, and she hasn't even made it into Tokyo U yet herself. It's her goal to get there, so his goal is to get there too because he admires her and is under the mistaken impression that she was the one who encouraged him by writing on his eraser. I don't think he ever actually said he has romantic feelings for her. You could argue it's implied by his focus on achieving the same goals as her and all that, but still. He never actually said he's got those kinds of feelings in regards to her, while on our end of things he has started considering whether he has feelings for Megumi.
I can see it playing out that Manabu hurts Megumi because when He DOES meet senpai he WILL probably fawn over her just enough to give Megumi the wrong impression. Then we get [x] amount of chapters before he realizes that he actually LOVES Megumi.
This I absolutely agree with. You don't even have to be romantically inclined to give the impression you are when you're around someone, so if they do meet up and have anything resembling a good atmosphere going, Megumi will definitely see it and definitely read too much into it. Cue drama. Resolve drama. Mutual confessions between Manabu and Megumi,
tap that ass with the fury of a god roll credits.