It's because he's being an idiot, to be honest. It's his own fault- he ought to know she wants him to take things more seriously, to push himself more. But he pushes himself in every which way and ends up frustrated and tired, because he's not focusing. She's good to him when he's got his head on straight. The problem is, he doesn't keep his head on straight. He's still got so much more growing up to do.
The real world demands so much from us, and he just hasn't been keeping his head in the game, so to speak. I struggled with very similar things during my relationship with my ex, and just didn't take heed of her encouragements. Real relationships require us to keep improving ourselves and growing as people, and he just... felt about as aimless as usual.
He's the one that decided on the computer solution himself, but she was encouraging him to keep pushing himself for the club. He kept slacking on club activities, which resulted in him being overlooked for the things that Suzuka was able to do. He could have joined her, even, if he was as committed to his own athleticism. Sure, by the time they were together, it might have been too late, but he's the one that kept slacking.
They weren't communicating properly, either, which is the biggest detriment. He continued to dance around subjects when he shouldn't have. He didn't discuss things that involve them between just the two of them, instead relying on THAT STUPID HATTORI! A guy that's never had a serious relationship in his life! Sure, he's been with girls, but he's never been serious with them, and it's evidenced by the way he approaches every problem. And Yamato needed to be serious with Suzuka. And it actually was good, at points. They actually did work, to an extent, but he just wasn't putting in as much effort.
Why did he keep refusing to call her Suzuka, for instance? He has no trouble calling Yui by her given name, even though I don't think they have a future. To be honest, I still think he can work with Suzuka, he just wasn't actually ready for the relationship at the time. He's still immature. And he's going to realize, if he starts dating Yui, that she is even more immature, I suspect.