I haven't really gotten into the later characters, particularly the Hoenn arc, but I have enough to mention a character.
Red. Red is different than Ash/Satoshi in that of, he isn't as arrogant and understand his limitations with himself and Pokemon but his greatest strength is his empathy. Blue (Green in the American version) tricked him and pulled her stunts on him but he cared about her to try and help her as they faced off against the Rockets at Sliph despite the deceit (like the badge swap). And Blaine, Red knew the scientist was a Rocket but he helped out with Mewtwo anyway.
He doesn't have the bravado the Satoshi character has with his tasks (training Pokemon, stopping the Rocket-Dan), his stance and all this was stated best in the first real battle with Giovanni, he had to stop the Boss Rocket because he was the only one who could. No one else had the empathy or strength to gell the resolve to thwart the Rockets' grand schemes but Red who had enough of Surge's captivity of them, Koga's mockery of the dead in the Pokemon Tower and Sabrina's barbs about the expendability of the mutant Eevee experiment, he had enough and he had a right to feel his indignation. Satoshi, sometimes, but not really.
That plus his intellect, which shines as he hides in his nonchalance and caring, makes him a character, not a caricuture.
My secondary choice is Yellow, the hidden gender aside, Yellow was different as she was a pacifist and not hypocritical as she wanted to be actual friends with creatures, who she rather distained at first (glad to see that not everybody loves the little critters), and at the end, resented to have them in a battle for fear of having them hurt but not once did she lose sight of herself as Wataru's odd genocidal plan unfolded and shown him the truth.
Her mystery mixed with her empathy (literally) makes a unique extension of the Red character and taking it to a higher plateau.
So that's my choice. Or best two, whichever.