The supplication: "O Allah, we do not ask You to avert the decree, but we ask You for kindness in it." Is this Supplication Halal or Haram?

We are obliged to supplicate Allah, so when supplicating we comply with Allah's Ordainments, and making supplications that are reported in the authentic texts is better. And Allah Knows Best. 

What is the ruling on combining prayers at the Musala (Place for prayer) of a shopping center because of heavy rain, knowing that some people come from outside that center?

Praise be to Allah, the Lord of the Worlds.

If there is hardship in going back to that Musala at the time of Asr or Isha` prayers, then it is permissible to combine prayers in twos only (Duhr with Asr and Maghrib with Isha`). Kindly consider calling us. And Allah Knows Best.

Should I pick up the newspapers thrown at the street because they definitely contain sacred names?

All perfect praise be to Allah the Lord of the Worlds. May His peace and blessings be upon our Prophet Mohammad and upon all his family and companions.

The Messenger of Allah (PBUH) says: "Be mindful of Allah and He will protect you." Part of this is protecting whatever contains the name of Allah. Therefore, if you see a paper containing Allah's name thrown in the street, then you should grab it and similar papers, then burn them in a clean place. Doing so is permissible because Othman (May Allah be pleased with him) has burnt copies of the Quran which didn`t match the main Mus-haf. However, you aren`t required to collect every paper in the street. And Allah The Almighty Knows Best.

Is it permissible to make up missed prayers at the times in which praying is disliked?

All perfect praise be to Allah,The Lord of The Worlds                                                                                                                                                                        It is permissible to make up missed prayers at any time even that in which praying is disliked. Absolute supererogatory prayer is forbidden to be performed at the times in which praying is disliked, and this also applies to Ihram and Istikhara prayers. However, there is no harm in offering prayers in Mekah during those times. And Allah Knows Best.