NTR where MC has a huge fucking dick would be amazing. That would signify his imperfections in personality, not in physical difference, so that it'll truly be his fault if she cheats. And even better if the NTR antagonist is smaller. All this would mean he lost mentally, and he should truly feel bad about it. He got outplayed by someone else, with them being more fun to be around, for example. It'll serve as a lesson to MC and make him better, and it'll not be all that dumb of a choice for FeMC either. Good ending.
But if he was born with a small dick, why would he feel bad about it? Well yeah, that's unlucky, but that's not his problem, that's how nature made him, he can't do anything about it. Nothing to punish, nothing to judge.