To combat both of these the logical solution is to include as complete of an array of pre-made quests as you can think of, so the player can just select them instead of needing to create them, and can look through them to learn what actions they can quest-ify. And if you do that you're 3/4 of the way to the 'achievement quest system' I'm proposing anyway.
so you start by making user quests "one click" simple to trigger. would two clicks be acceptable, action and object? then the next step is to simply automatically track them all at all times, and give rewards as they are completed - similar to an achievements system which constantly checks conditions. that's the idea you're talking about?
that would automatically reward the player for any type of gameplay they prefer, assuming you had a predefined quest that covered whatever they were doing. but it doesn't expressly create a link between "i need X, so Y is my goal. so i do Z" its more like "look, the player has done a lot of Z, reward them!". i mean, i gather a lot of nuts and herbs for food, healing, and sacrifices, but arrows are what i need. and again, those rewards are in there, but on a per action basis, not in chunks. and sometimes the anticipation can be great even for a single action. while there's not much anticipation while waiting to see if you succeed in making a single wood arrow, its a very different story for something like a storage pit or hut, which is a major undertaking.
i see what you mean about there being little difference between user quests and automatic rewards, mostly ease of use issues.
perhaps approach it with a different trigger question:
if the player can do anything they want and will be appropriately rewarded no matter what they choose, how to reflect that one action is more important to the player than another, and therefore provide a greater reward for such actions?
one way is to make all rewards higher. that way a player gets X rewards for doing some subset of the possible activities (the ones they like), as opposed to X rewards for doing all activities about the same amount. but that doesn't actually change things, it just scales them.
so maybe the existing system which rewards all activities appropriately is enough? if the player needs arrows, they'll make arrows, and get mood boost and woodworking exp as a reward, but nothing special for having 20 arrows for each archer band member, other than the fact that their archers now have arrows, so lookout world! <g>. FYI it takes about a dozen wood arrows to take down a single camelops (american camel).