I'd prefer they go with a CONSISTENT style. Regardless of whether it's artwork or 3D. If they're going to show artwork, then show it for all of the trainers, even the important ones. And if they're going to show 3D, then give each trainer their own 3D model and show a Pokeball throwing animation. It's very jarring to have three different styles in contrast; a low-resolution overworld model, a high-resolution battle model, and a random generic Sugimori artwork.
I'm of the opinion that the artwork should be phased out. And don't really think that much would happen to Mr. Sugimori if they did so. He'd definitely still have his job, because his artwork is important. It makes it easy to show what all the Pokemon look like outside of the game and he'd still have a huge load of work to do regardless.
I think they'll probably stay with the 2D artwork until the next generation, in which case they will be more experienced and comfortable with 3D and be converting most to 3D models. Could be wrong, but it just seems most likely to me.