TBH,For me it's a 3 way tie between Alder,Blue and Cynthia. Blue is the original champion,the guy that was always that 1 step ahead of you. The moment you think you finally surpassed him and have become the champion,Lance drops that bombshell on you. You're rival was the champion,HE was the final boss of the game. Alder is just awesome,so laid back,and that hair animation though. There's also the fact that he uses some of the lesser Gen 5 pokemon with a focus around his signature Volcarona. Then there's the fact that he is the first important character to have been confirmed to have a deceased pokemon,his starter no less. Cynthia is just a boss. nothing more,nothing less.
Battle theme wise,it's the same three way tie,Alder has laidback style but he used pokemon that he raised from the ground up,they've been with him for over 40 years and it shows by how strong they are. Blue is just a boss and Cynthia's theme is climactic. Bad ass and it shows when her Garchomp comes out.