Just look up the flowchart. Do the quest if you have the items on hand already, or when you're bound to go to that specific location anyway. I ended up doing quite a bit of quests, but I never farmed. I have one maxed weapon, which is weak AF though. And a level 3 Phoenix spear and a few level 2 swords that demolished the endgame on Hard mode anyway. Quests are mainly for money, and you don't need that much in the end (you can also sell items you won't use). I could buy all weapons with quite some quests left unfinished (shit, like catching 10 fishes, get 10 alloys, and some other stuff I ignored). There is one quest, or maybe 2, that grant you a weapon and thus are required for the true ending. But that quest was decent actually.
Some are fun, like the sick kid you can easily do when the story takes you to the tree anyway. I thought the bandits quest was nice as well, basically some combat challenges to mix things up.
The biggest bitch is farming Eagle Eggs (and its impossible to do after a certain event), though you can use other weapons if desired. But I like the Phoenix set. You can get them from the third DLC door though.