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.

Does fasting on behalf of a deceased person permissible?

Fasting on belhaf of a deceased person is permissible, since the Prophet (PBUH) said: "Whoever dies while he still has some fasts to make up (of the days of Ramadan), then his heir (any of them) should fast on his behalf." [Agreed upon]. The previous answer is for making up missed obligatory fasts on behalf of the deceased. But if the fasting on behlaf of the deceased was for performing  a voluntary acts of devotion such as fasting....is permissible as adopted by the majority of Muslim scholars and based on the above hadith as they stated "Every good dead intended to be on behalf of the deceased its reward will reach the latter." And Allah Knows Best.  

Is supplicating in Qunoot, at times of affliction, during obligatory and voluntary prayer a Sunnah, and should it be done before Rukoo` (bowing), or after it?

At times of affliction, it is a Sunnah that Muslims supplicate in Qunoot after the final Rukoo` of each obligatory, or voluntary prayer as individuals, or in congregation.

Does offering Udhiyah (Offering a Sacrificial animal at Aid Al-Adha) avails from offering Aqiqa?

Offering an Udhiyah doesn't avail a person from offering Aqiqa because each of which is a different act of worship. And Allah Knows Best.