How this would work:-
This would affect the character info box with the stats, all it would do is highlight the text (and numbers if you want) that is being affected by your nature, red text color to indicate the decreasing stat and green text color to indicate the increasing stat.

Just for clarity, lets say that the below stats was for someone who has Rash nature (Rash nature increases Sp. atk and lowers Sp. def). The font colors would look something like this:-

Attack
Defense
Sp. Atk
Sp. Def
Speed

See below picture of this system being used in the handheld Pokegames, heartgold/soulsilver, the nature of these stats are careful



Credits goes to Zete for coming up with the idea, I'm just posting what he thought would be a nice feature to have.

On a side note, in official games the blue stat is the stat being decreased, and the red stat is the one being increased, So ugh... probs would seem more legit if you went with it being the other way round.

Thanks for the credit :3 

The blue and red thing the original games do is confusing to me, I'd rather have red and green - psycologically the idea comes clearer to the players.

Great idea.xD