If we're taking artistic direction, then Otomo hands down. But Miyazaki's movies are generally more imaginative (mostly because he's been more prolific). Overall, I'd probably go with Otomo; the protagonists in Miazaki's films are usually laughable and always forgettable.
You have some truth, but I feel, that both of their characters are pretty laughable. "Steamboy," "Kanada,"...truth be told they are no better than Ashitaka or Chihiro. In fact, Ashitaka and Chihiro are not forgettable and might be better "protagonists" than Ray Steam, Kanada, or the boy from Cannon Fodder. But...Tetsuo is probably one of the greatest villains of all time. I wonder who would win Tetsuo or The Joker?
That's somewhat of a hard comparison to make since I haven't seen much of Otomo's production - limited as it is. I've seen Akira and Steamboy, both of which I liked, but which are also very different in character. Akira was much more a gritty cyberpunk piece of apocalyptica whereas Steamboy is much more adventure-based action to almost Hollywood levels of convention. I've also seen his collab project Memories, the third segment of which he directed himself, and which I also liked quite well. But ultimately his involvement in the more substantial parts of that anthology were rather confined, even if it was basically his project.
Miyazaki, on the other hand, is neither that gritty nor willing to do much outside of either slice-of-life or generally comedic fantasy. There are exceptions, most notably Princess Mononoke (being my favourite film from him), but I could never see him doing a film of the same temperament as Akira (Isao Takahata on the other hand...). But then again, neither could I really see Otomo pulling off the type of whimsical adventure Miyazaki is so adept at doing, so again it's somewhat of a tough comparison. Though I will say Miyazaki to me hasn't really been able to top Mononoke with any of his later films, including the much-adored Spirited Away.
However, I will say that I think both of their manga versions of Akira and Nausicaa of the Valley of the Wind are top notch masterpieces, and both are much superior to their respective film counterparts by virtue of having more time to flesh out the intricacies of the stories. But even here it kind of just evens out to the same level with both being just as good.
So which one would I prefer? I guess I'd have to say Miyazaki by virtue of having quantity on his side, and with Castle of Cagliostro, Laputa and Mononoke being excellent films all round for me. Otomo's Akira somewhat looses out to the manga version and Steamboy lacks the flair of truly great films (+ I haven't seen much else from him) tips the scales more in Miyazaki's favour in this.
But I still prefer Satoshi Kon over either of these two.
You make a really compelling point. I also like your little twist at the end about Satoshi. It seems that these three are probably the kings of Japanese animation in terms of style, story, and presentation. Momaru Oshii, Yoshiaki Kawajiri, and Takeshi Koike are also some of my favorites but they don't have the same visceral impact that the former three have. Koji Morimoto is also really good, but he just needs to find a good simple story and direct it. I thought Magnetic Rose was phenomenal.