*Note that this Trophy can be bought in the resistance camp after playthrough 3*
Solution not using the shop found below
Almost every side quest in the game is marked by a red dot on the map so they are easy enough to find. Even if you don't find the couple of quests that aren't as easily found, you will be able to get more than 80% by the time you finish the three play-throughs that are required to get all of the story trophies.
When you first start the game, you can't fast travel so it is best to leave side quests at first. Some side quests available on the first playthrough have enemies far higher level than you and take quite some time to kill so the most efficient way would likely be to leave most of the side quests to the second playthrough and beyond.