A cute manga like this could have a lot of elements. Maybe it shows how their relationship changes the perspectives of those around them. Or it could have funny scenes as they navigate through life with their differences.
There's 'Revenge of an Ugly Girl' where the main character is considered ugly but has a powerful story of growth and self-acceptance.
One such manga could be 'Ugly Duckling's Love Story'. It focuses on an ugly girl's journey of self-acceptance and finding love.
Maybe she undergoes a personality transformation that makes her more confident and charming, which in turn makes her appear cute. Or it could be that she discovers her hidden talents and that boosts her self-esteem and attractiveness.
Possibly, it could be a tale of them working towards a common goal. For instance, participating in a competition or solving a mystery. Or it might focus on their differences and how they learn from each other.
Often, such a shoujo manga might explore themes of friendship and finding true love despite the girl's unconventional looks. It could also show her developing unique talents or skills that make her stand out.
There are many possibilities. Maybe a comedy manga where their appearance contrast leads to funny situations.
I recommend 'Pochamani'. In this manga, a cute girl has a dog as her companion. The story shows their close bond and adventures together.
It could be a tale of unexpected romance between a student and an unconventional, less attractive boy, exploring the challenges and emotions they face.
You might want to check out 'Mysterious Paintball'. In this manga, a girl dresses as a boy to participate in paintball competitions and uncovers hidden secrets along the way. The plot is full of twists and turns.
I think 'Kaguya-sama: Love is War' is quite popular. It has a great mix of a boy and a girl's storylines.