She Was Pretty, Cheese in the Trap and Attention Love seem to fit best. Thanks for these.
The girls in True Beauty, Accidentally in Love and Ugly Duckling aren't ugly. If anything, they look better than average. The girls don't have to be "ugly". They just have to be ordinary and their plus point for the male lead should be their personality or even attitude.
As for cross-dressing, I presume that has more to do with sexuality rather than looks. Especially if the male lead doesn't know that the person he is falling for is a female.
The highlight of their relationship should be that he likes her for her personality not because she is trying to be more pretty or that she changed her looks to become more attractive. If anything, he should like her the way she is. Sort of like in Extraordinary Attorney Woo, he likes her quirks or despite that. But the show doesn't explore the relationship much. Also, she is quite brilliant which is far from being a plain Jane.