The majority of the trophies are tied to Power Cell tasks within specific areas. I will group them in order to give you a general idea of what to look out for, though it would be in your best interest to clear all Precursor Orbs, Power Cells, and Scout Flies when you get to the areas in the first place. Some exceptions will be when you need Blue Eco Vents or Yellow Eco Vents, as they will require you to toggle some buttons that are only in specific locations (Blue Eco Tower in Forbidden Jungle, Yellow Eco Substation in Snowy Mountain).
Geyser Rock: (Can't Miss)
Sandover Village:
Sentinel Beach:
Forbidden Jungle:
Misty Island:
Fire Canyon:
Precursor Basin:
Boggy Swamp:
Mountain Pass:
Spider Cave:
Snowy Mountain:
Lava Tube:
Dark Citadel:
If you manage to collect all of the Precursor Orbs, you will also collect:
If you collect all of the Scout Flies, you will collect Power Cells as well as the following trophies:
By collecting all of the Power Cells, some of which are necessary for story progression, you will also finish:
The last trophies you get might depend on your play style. Some instances, it might be the story battle against Gol and Maia, meaning you've already collected all 101 Power Cells prior to the battle. Or, it might be the Precursor Orbs, Power Cells, and/or the Scout Flies, as they can be rather difficult to find sometimes. For the most part, the game itself can be completed within a few hours if you truly focus on one task at a time (and it is convenient that they provide you with information in the Start Menu).