How about I take you through a bit of what I've been developing for a Pokemon d20 game?
Pokemon:
HP: The same as in D&D. If you hit 0, you're unconscious, negative 10 is death under book rules.
PP: Would be more like mental HP in a pen and paper, which would follow the Anime more accurately. Pokemon have been known to lose consciousness just by using too many attacks in the Anime. Aside from that, in Pen and Paper, it would be used for all attacks, like a Psionicist's Skills, using up a number of points, based on how powerful you'd want to make the attack. Each Attack would in turn have a description, illustrating the base damage, and how many points it uses to reach each degree of damage.
Four Stats: The GB games, believe it or not, almost do this one for you. A Level 1 Pokemon usually** has between 9 and 20 Points on average for each skill, so it would be broken down into the 3rd Edition Rule Set. It would probably look something like this:
Score.........Modifier
1.................-5
2.................-4
3.................-4
4.................-3
5.................-3
6.................-2
7.................-2
8.................-1
9.................-1
10.................0
11.................0
12................+1
13................+1
14................+2
15................+2
16................+3
17................+3
18................+4
19................+4
20................+5
And, as in D&D, the modifiers are used in accordance with what fits the stat.
Attack:
-Hit Rate
-Damage of Melee Attack Types
Endurance:
-(It used to be called defense, I believe)
-In any event, how well you withstand damage
-How well you withstand Physical Status Effects, like Poison, Paralyze*, Burn, etc... (Fortitude Saving Throw)
-Can also modify how many HP you get per level, but that already seems to be set in stone pretty good (usually about 1-10)
Agility:
-How hard you are to hit
-Whether or not you go sooner in a combat round
-*Could be associated with resistance to paralysis, or avoiding certain special attacks (Reflex Saving Throw...)
-Possibly Ranged Attack, but that could also be in the Attack Category
Special:
Basically, this seems to be the intelligence of the creature, so it could be associated with everything else.
-Skills (if you use a Skill Subset like in D&D)
-Any Mind-Type Status Effects, such as Confusion, Sleep, etc... (Willpower Saving Throw)
-Possibly, whether you can learn a new attack or not (I didn't think it made much sense to go strictly on Level for this one)
-Whether or not your Pokemon can understand others' languages (There is no universal Pokemon Language)
Charisma:
Believe it or not, the series uses this one.
-How well your Pokemon gets along with other Pokemon; higher Charisma makes it easier to interact with various Pokemon
This brings me to the next fundamental element:
Trainers:
Since these are your Player Characters, you'll need to know how to run them.
These are the characters that'll use Alignment and Charisma often. All of the stats are very similar, except that Trainers don't really Attack, but they can still be hurt, as has been shown in the series many a time.
Also, these characters will gain levels like the Pokemon. Why you ask?
Why did Ash not know a thing about what he was doing initially, but is now a veteran? Experience. Trainers gain experience just as Pokemon do. And as a result, they gain stats and HP just the same.
Trainers use the following Stats:
Strength
Endurance
Agility
Intelligence
Charisma
Strength is usually associated with skills and rarely fighting. Usually, the Trainer is in the back, calling out Pokemon and supporting them, but what about climbing a mountain? Endurance determines how successful you are. How about carrying heavy objects? Strength can tell alot regarding this.
And there's Charisma. How well is the Trainer going to get along with their Pokemon? This is used alot in Pokemon. Not only does it determine how well you get along with a Pokemon, but it can also determine how difficult it is to get a Pokemon on your side without capturing it.
Finally, we come to catching Pokemon. You simply use the percentile dice here. You get bonuses based on how low the Pokemon is on HP, how many Ranks your Trainer's Capture Skill has, and the type of Ball you're using. (DMs, never give a Master Ball to Trainers. It's considered a Major Artifact.)
Legendary Pokemon: These are esentially God-Like characters in the Pokemon world and should be run as such. I need not say more about them.
This was a summary of some of my workings that I've been developing. While they are nowhere near complete (Anyone know all the Attacks?), the systems that I have come up with work so far.
**4d6 should get you between 9 and 20 points, but Pokemon in the games have been known to start higher occasionally.
