The plethora of herb skills is indeed nutty.. I use all the skills and just look at them a specialties/complementary skills.
Flora Lore would recognize some herbs (common ones)... but this isn't a herb skill... a PC can recognize a herb, but dosen't really know how it works... so wouldn't know to apply it externally or internally, brew it or eat it...
Herb Lore. This is complete knowledge as to herbs... and what gives them their effective result. Herb lore will identify herbs found, and be very useful when foraging. This also includes knowledge of what makes a herb effective, so helps in the preparation process and application... I give a +1 bonus to each, prepare and using prepared herb skills for each rank in herb lore.
Prepare Herbs. This is the process of transforming the herb from its raw state to a purified state, it as much a crafting skill as a knowledge. It can also allow the user to attempt to concentrate herbs, making them more potent, combine herbs (into for example, one tea that has the effect of two distinct herbs), change the herbs method of application, as well as make other 'on-the-fly' tweaks. Obviously herb knowledge is a necessity here and well as application... so again, each rank in this skill gives a +1 bonus to Herb Lore and Using Prepared Herbs.
Using Prepared Herbs. This skill I think of as knowing how to get maximum effect from herbs... I think of it like the knowledge that a pharmacist has... he knows how much you should take and when. To make this skill useful I call the listed effects for herbs, the optimum effect. A town healer/herbalist might sell a PC herbs and tell them how to use them to deal with one bleeding location, or one specific poison. But unless he's addressing the same problem, with the same herb, and same quality of herb, the PC's got to use this skill. Think of herbs, not a bandages, or potions, but as drugs. Lack of this skill or utter failure would result in the herb only being 50% effective, or even completely wasted, it could even cause a side effect... (ie: most anti-biotics will fight an infection, however the use of the wrong ones will meet with more limited results, and possibly cause other side effects like digestive tract problems)... again, because of the large number of herb skills, I give +1 to Herb Lore and Preparation for each rank in this skill.