I realize answering this answer is 3 months late, but here's what I've figured out playing around with it:
If you are not running a very social heavy campaign plan to make Discovery DCs on the easy side. Also add more Discovery skills. Ultimate Intrigue (UI) says it usually is Sense Motive, but the PCs I play with usually don't put a lot of ranks in it, so the ones I've added are:
-Diplomacy to gather information from other NPCs about the NPC in question if the situation allows.
-Diplomacy just to converse with the NPC about their interests.
-Perception (maybe noticing items around their household or on their person that could give clues to their interests)
Bardic Knowledge
Plan to give an NPC at least as many Influence Skills as successes needed to gain influence in addition to diplomacy.
Knowledges and Professions will be your friend for that.
The lore skill from Pathfinder Unchained is a good double up for Knowledge skills. Using the Background Skills rules from it is also a good way to make sure PCs have a selection of useful skills for this system.
Several skill can stand in place of knowledge skills, Survival for nature, Spellcraft for Arcana and Religion, Appraise and Craft could fill in for a profession in some situations, and Bluff, if rolled well, could really stand in for everything.
The way I handle Diplomacy is that in order to use it to gain influence you need to know a weakness of the NPC and say you're using it with your diplomacy roll. Unlike other Influence Skills, which can only be used once successfully per social encounter (if I'm remembering right), Diplomacy can be used multiple times, but each time it is used a new weakness must be used.
Have a handy list of weaknesses/strengths to pull from. Here's mine, feel free to add to it:
Flirting, Joking (high/low brow), Stories (sad, happy, true, legends, etc), Bragging/posturing, Inspiring speeches, Compliments/Flattery, appeals to morality, appeals to ego, appeals to desires (food, sex, money, etc.), appeals to logic
Intimidate can be used like Diplomacy if the character is particularly weak willed. While the intimidate skill normally only lasts for a short amount of time and makes an NPC dislike you afterwards, using Intimidate in this way could be used in a classic Disney Villain/Henchman situation. Intimidate has its own list of 'tactics' like Diplomacy:
Bragging, taunting, insulting, physically threatening, explaining dire consequences
I've also added a few other categories that could be used to gain influence beyond rolling for skills.
-Challenges: Does your NPC like to drink? PCs could get a success for being able to drink with them all night. Are they fighters who like sparring? Go 3 rounds in a boxing type fight.
-Gifts: There are several ways to handle gifts. Some NPCs just like expensive baubles, and a particularly expensive gift could count as a success. Maybe they have a love of Elven weaponry, or ancient tomes. This is a good way to make Art Items from the loot list more important and meaningful to treasure hoards. Normally no one cares if you find 3 silver candle sticks, but if there's an NPC collecting Chelaxian Antiques, then all of a sudden they become useful.
That's all I've got at the moment. If I have anything else I'll reply again. I hope these things help!