Nearly all the buttons for gatherers serve their purpose; there are some that overwrite each other, but not many. Think of all of these skills as tools like wrenches, and you choose one based on the size of the bolt. You might not use tools like Field Mastery III/Sharp Vision III much, but you still need them when the time comes otherwise you will struggle trying to get a job done with an inadequate tool. I hope that makes sense.

The usability of all the buttons is contingent on the goal of your gatherer on any particular gathering trip. Sometimes you're after yield; other times you want HQ, and other times you are uncovering what a node will give. In any case whatever your goal is, you will want to spend your GP towards that goal. If you are after yield, look for nodes with +1/+2 gathering attempts and exhaust all your GP on that node. If you after HQ, look for nodes with that bonus and apply the appropriate skills to that node.

Excluding skills associated with collectables, you basically can place all those skills into four categories: You have skills that increase yield; skills that increase HQ chance; skills that increase your gathering rate; and lastly are enhancements with a myriad of effects such as granting another attempt, locating nodes, stealth, etc. Yield, HQ, and gathering rate skills are tiered and it is a very good thing they are so you can choose the appropriate increase depending on the node.

Your appraisal skills for collectibles is a bit of a different ballgame. I won't get too much into it, but the simplest way to explain those is you need to get the gathering rate to 100% and still have 600 GP in order to take full advantage of the node.