Yes, I know. We have discussed it in the past. The problem with the current system is that you either have to siege or be able to check your plants daily in order to get some of the mats needed for higher level crafting. There just are enough hours in the day to gather enough stuff to make it worthwhile except as a means to level your gathering.
The obvious problem with upgrading pet craft levels- pretty soon you are making mats worth more than the pet tools and it becomes a mint for game gold. Bad idea. I have noticed though the the pet autocraft add-on has options for small pet tools, medium pet tools, and large pet tools. RW could add medium and large tools with higher gold costs. For example, the medium tool could be priced around 225 to 240, and give mats up to level 110 or so. The "garbage" mats that consume half your tools and slow the process down( assuming that's why there are there), produced with medium tools could be worth maybe 5 gold more than the tools, and then the return on these items is even a smaller percentage of what the small tool garbage gives.
Then, when we are at a much higher level, RW could add the large tools.
Problem solved.