So on to the main character, and stats.
Name (well, obviously right?) - no game effect. This should get referenced a lot by other subroutines because its really sloppy to have the entire world refer to the player as "hey you" or "the Courier" for the entire game, right?
Fame - how well known you and your services are. Almost every action in town should increase or decrease fame according to results. Fame will be directly related to customers showing up, random events, and the different shops and services being offered.
Reputation - Should be a separate page because your going to get a reputation for each NPC and group in the game. Most NPCs will belong to a group. When you interact with a NPC you are going to receive a reputation plus or minus for that NPC, and a lesser reputation bump for the group. Lets say there is a Team Rocket member named Cassy you deal with. Depending on what decisions you make you could get a +10 mod for Cassy and a +1 mod for Team Rocket, or a -15 mod for Cassy and a -2 mod for Team Rocket (probably negative mods should be slightly higher than positive). Later on the police are after Cassy and you can choose which side you'll help, which gives +10 for the one you help, and -15 for the one you don't. Casual conversations should give a +1 mod. Talking with people about nothing tends to make them like you a little. Also your wasting time you could use to really improve things. Merchants should give a +1 every time you buy something, and at high levels offer a discount on some services or a new service.
Toughness - a combined strength and endurance stat for combat. This isn't the focus of the game so simplifying player vs NPC combat is probably best. Higher stat means more combat damage from non-pokemon attacks (probably referred to as 'attack' in the combat menu), and it directly corresponds to the player's HP. Can be trained in the Gym and Dojo, or with weights and improved with weapons and protective clothing.
Charisma - Ability to talk people into doing things. High charisma will allow you to work in public places without drawing the attention of the police or rivals. Higher charisma will open up more conversation options. Stat is raised by talking to NPCs and successfully getting 'charm' results, and by wearing impressive clothing.
Business - The ability to work deals with people. Has no effect on shops. It does affect how much you get for tricks, and the prices non-shop NPCs offer. Business should be used as a direct modifier to a NPC's offers. So for payments to the player it would be (default price x {1 + [business/100]}). So if the default price for a Dirt Digger is 10 yen, and you have 10 business you'd get (10 x 1.1) 11 yen. Round everything to the nearest whole yen. Oh, the Pokémon world uses yen and I say stick with that.
You improve business by making deals. Tricks should add about 1/10th of a point, buying a new apartment and deals with random encounters should add a whole point. Business attire also gives a bonus.
Training - Your ability to train Pokémon. As you gain ranks you'll gain the ability to teach new moves to your Pokémon. Also your train action gives a Pokémon a certain amount of xp. Training is raised by training your Pokémon, reading books on the subject, talking with other trainers, and also by pimping your pokemon. Training should give about a half point per session. Pimping should be 1/10 of a point. Books could offer 2 points per read and can be read 5 times to finish the book (so +10 in 5 hours). Talking with other trainers (random encounter?) should add around 5 points, and be rare. Training supplies (sex toys) should offer a boost but no new moves. New moves should be offered say every 10 points, and by doing quests.
Health - starts at 100 and is totally separate from HP. This is your overall health and it should only change slowly. If you don't take care of your own health this will result in your overall performance decreasing. Mainly this stat is decreased by a failure to fulfill other needs, random encounters, and loosing battles. The main way to increase this is to sleep with all other needs fulfilled. Each night you gain 1 point for each need filled (over 70), and loose 1 point for each need not filled (under 40). Needs are Hunger, Joy, and Energy. All these Needs stats should range from 110-1. If you go to zero in any of the need stats, its game over via stupidity.
Hunger - starts at 100, decreases as the character does stuff. Unless the character is eating hunger goes down 1 point per hour + an amount for what the character is doing. That means you get 8 hunger for sleeping or waiting 8 hours! Walking should double that, battling should be at least +3 hunger. Pimping a Pokémon basically means light conversation unless things turn ugly, so probably no additional hunger for that. Eating brings this stat up, the better the food the more hunger is relieved. There are no permanent items to restore hunger, but you should be able to carry some food items like (human) candy, drinks, and snacks. Carried food items should be expensive compared to the amount of hunger they restore. If your hungry, you should look for a restaurant.
Joy - starts at 100, decreases as the character does work. Doing anything while another need is under 40 causes -1 joy per need under 40. Keep track of a character's last 20 activities. If a character does the same action 10 times, -1 joy from continuing to do it and you get a "bored" message. Keep track of the last 30 meals. If a character has 10 of the same meal on the list, -1 joy and another "bored" message. Same for increasing joy. Resting activities don't get tracked, no getting "bored" of sleep or TV. Anything stressful subtracts from joy. Sex, drinking, partying, talking to girls, and other "fun" activities add to joy. Some rest activities should overlap, like watching TV (big energy boost, small joy boost). Some furniture items should give a permanent boost to your max joy, and how much joy you get from an activity. Like a Big TV would add an extra +1 joy when you watch TV. You should be able to buy a video game for your Pokedex so you can Play Game instead of rest, which gives you some joy but less Energy.
Energy - starts at 100, decreases the more active you are. This stat should be easy to shift up and down. You should be able to REST anywhere, but run a chance of random encounters after you rest finishes. a lot of activities won't really affect energy if you aren't moving. Pimping is a spectator sport, but your not exactly resting so it should be a no change. Walking is a slight decrease in town, and a significant decrease out of town or in dangerous locations. Some locations should have better rest activities, like at home you can watch TV to rest and get a slight joy boost. Eating should restore small amounts of energy as well as restore hunger. Buying better furniture will give you more Energy. Buying a better bed will increase your max Energy.
Money - well, its technically a stat. Shouldn't ever go below zero. No max.
More stats could be added later. I think that should be enough to work with.
New Stat added! Perception - starts at 10, increases through use. This stat should generally go up with use. Can be trained by going to public locations and "people watching". At 10 when you Examine a NPC you get Name and HP, and the top Trait. Every 5 points you get an additional trait (if they have one). At 25 you see how much they pay for a trick. At 50 you get the NPCs stat block. At 80 you can see the NPCs factions. At 100 you can see the NPCs skill list! Perception only decreases as a result of using certain items, or events.