Let's see, since I only like the Pokemon Adventure manga while I hate the anime, I'll have to go with Red, being the only protagonist trainer in the manga and all...
But that's simply of how good he is at battling, his character and his history with what Pokemon he has encountered, basically capturing things like Mewtwo and fighting Deoxys and even a fusion of Articuno, Zapdos and Moltres! Additionally, he beat Bruno's entire team with just his Eevee, which can evolve and devolve at will, but who cares?
From other trainers in the manga I really like Giovanni for how cool and smart he was behaving, be it when battling or when just doing nothing big (eg: fossil mining) and also how he was above Elite 4 level as a battler, with them being too scared to fight him even 4 to 1 and having to lurk around, plus how he was so cold-hearted and vicious during gym battles that challengers often ended up dead!
However, if I had to pick an anime trainer, I guess I'll go with Cynthia, considering how she's the champion and all and how I like Garchomp, but to be honest she's just average compared to the ones in the manga, just best from the anime...
PS: Honorable mention is Pryce from the manga, having owned all 3 legendary birds, Ho-oh, Lugia and Celebi, even if some were only temporarily, along with his already really strong Ice type Pokemon and being a master battler too and all...