The order I'd use

The order I'd use First, play the story and do side activities when you actually want a change of pace. You don't need to clear every available marker before the next mission. More activities and abilities appear as the story moves forward, so trying to force a perfect district too early can just create unnecessary backtracking. Second, make a habit of using both characters' combat systems. Peter's mechanical arms and Miles's blue Evolved Venom abilities each have a 100-enemy requirement. If you never equip one of those sets, you can finish a lot of the game and still have that counter waiting for you. Third, use Web Lines for stealth once they unlock. Twenty-five takedowns from those lines are easier to work into normal stealth encounters than to remember only after you have cleared the map. Fourth, finish the story, then work district by district through the remaining map counters. Some quest lines have a concluding mission after the initial activities, so follow their messages and final markers instead of stopping when the first batch disappears. Fifth, spend your earned resources on the required suits, gadgets, and Suit Tech; clean up the sightseeing and traversal challenges; then start NG+ if you want the added trophy or the complete Steam set. That keeps the second run from turning into a repetition of side work you already finished. The NG+ award is for finishing its main story, not for repeating every district at 100%.