Hope just some expanation:
Guildheists - Yes they are suppose to teach you how to party play, but they are really nothing more than an exp boost now. People do guildheist roulettes everyday for the exp and GC seals.

Potions - For end game raiders - no matter if it is the +STR/DEX/INT potions to squeeze out that extra damage to pass a DPS check or just MP pot to let out that extra flare, people use it.

Food - Again, more useful for progression raiders like the Binding Coil when it has no echo or nerfs - any extra damage, any extra HP (it can add a few hundred) helps surviving stuff.

Chocobo fighting - Just a companion to help you kill things fasters and/or heal you. They aren't that much help but better than nothing. Example: it allowed me to kill lv59 mobs at lv50 for daily marks because my bird heals me.

Hunting/Sightseeing logs - Both Exp boosts, and achievement for those people that care about achievement points and stuff. It helps leveling especially before all the exp boost, roulettes and other stuff that came out.

City to City Airships - I think it was more for the story component - I would say for your first time traveling from 1 city to another, you used the airship and not walked there as you didn't have the aetheryte attuned yet.

Treasure Chests - What's wrong with it? To get gear and stuff?

Linkshells - I have multiple linkshells, talking to friends outside of the FC or raids or for hunts. Some friends I made were in their own FC already, Linkshell give me an easier way to communicate.

Irrelevant quest lines (Ultima's Bane, Relic Weapon, etc) - Relic weapons were top tier weapons, fully upgraded at lv50 was even better than Dreadwyrm weapon - the best raid weapon. And other Primal/Ultima fights provided gear/weapons for players - unfortunately became irrelevant once the ilvl raises in vertical progression game.