I'd have to say my absolute favorite is Gary Oak.
In my opinion, he's really the strongest trainer in the entire anime. In a world where justice reigned supreme, Gary would be the star of the anime, not Ash. I like him waaaay more than Ash for three reasons:
1. He actually matures. Unlike Ash, who does show growth as a trainer, Gary shows growth as a trainer and a person. As time went by, he actually changed. In the beginning he was stuck up, conceited, arrogant, and somewhat mean to Ash. (He was still pretty cool, though.) But as time went by in the anime, he matured, grew more humble, and a lot stronger as a trainer. He still had a bit of an arrogant streak in him though, which made him all the more appealing. Ash's character never changes or grows, which make him boring and so very same ol', same ol'. Gary's character is more realistic and interesting, as he doesn't stop maturing.
2. He's very intelligent. In the beginning before he faced the first Pokemon League in Kanto, he was smart enough to study gym leaders and their habits so he could know which pokemon to use against them. Professor Oak was extremely impressed, pleased, and proud by this. I remember his words "Excellent strategy! That's my grandson! ^^" He's a great strategist. He's quick on his feet and knows how to use what he's learned. And he learns a LOT. That's what's going to make him an awesome researcher.
3. He's powerful as a trainer. He has only lost one battle against Ash (in the Johto league), and Ash very barely won that one. In all the other battles he's had with Ash, he soundly trounced his rival with ease. Even as a researcher he's still an extremely powerful trainer. His brand new Electovire ripped Ash's Pikachu a new one. Not bad, seeing as how Pikachu is grossly overpowered and Ash's starter at that. And it was thanks to Gary Ash was able to help train his Gliscor, once again showing Gary's superior abilities as a trainer. And don't even get me started on how awesome sauce his Umbreon is. ^^
My second favorite character would have to be Paul. He's harsh and tough on his Pokemon, but he also works hard and trains harder. His mindset is one of a warrior, and I like that about him. He reminds me of Silver for a lot of reasons.
P.S.: How come Silver has never made an appearance in the anime???? :(