Is it permissible for one to shake hands with his uncle`s daughter?

No, it isn`t because he is a non-Mahram (Marriageable) to her.

Is it incumbent on the fiancée to obey her fiancé?

When the woman settles in her husband`s house, it is incumbent on him to provide for her and it is incumbent on her to obey him. Before that, and if the marriage contract had been concluded, then she is lawfully his wife and thus she should abide by custom in treating him, but if the marriage contract hadn`t been concluded, then she should treat him as a non-Mahram (Marriageable).

Generally speaking, I`m dutiful to my mother and opt for obeying her. However, she chose a certain girl to be my future wife, but I`m not pleased with her choice although that girl comes from a good family and enjoys good character. Should I obey my mother or choose another girl that lives up to my expectations?

Praise be to Allah the Lord of the Worlds.

One must obey their parents in whatever is in compliance with the teachings of Sharia and within one`s capacity. However, you aren`t to blame for not marrying that girl, but it is better that you tell your mother about that and it is preferable that you perform Istikharah prayer. And Allah The Almighty Knows Best.

Is it permissible for a person who has to make up for missed fasts to fast six days of Shawwal (the month directly after Ramadan) before making up for the missed fasts?

Yes, it is permissible for him/her to do so, but it is better that they make up for missed fasts first. And Allah Knows Best.