One problem I've ran into personally is the different quest types. You have your active quest, main quests, side quests, errands and you can add jobs. Jobs is the odd one where you can set a quest for gathering the required items to craft a pouch upgrade for example but there is no jobs option in the menu. It appears under errands which is odd since it specifically says "create a job". I just find there to be too many headings under quests.
A few things I picked up along the way is to always kill animals you see(not necessarily mechs). The xp adds up quickly and the extra resources for crafting and trading are never wasted. Don't forget to scan the water once in a while for fish too, you will need fish bones etc to craft certain items. Also gather all the resources you come across. Skipping them for the sake of time can hurt when you want to craft elemental bombs or arrows. I find resource gathering/hunting very annoying but have come to accept it as a critical part of the game. Don't forget to upgrade your inventory pouches. You can do this right from the beginning in crafting and I never found a tutorial that mentioned it at all. When you buy a new weapon, do the tutorial quest to learn it's usefulness and get free XP. Don't forget to trade in resources to merchants for metal shards. This is your currency and some items are worth quite a few shards and are acquired easily. There are some items that have no crafting usage, sell these.