Emphasis would be on environment, plot progression, battle, and music.
The world itself would be as imposing and wild as possible, stretching great distances and presenting the viewer with a sense of grand scale, giving the characters interesting lands to set their stories in.
The style would be similar to Origins, focusing on smooth animation and color theory that would give it a vibrant, somewhat realistic feel rather than a toony one.
The presentation of pokemon would be that they are still wild animals, rather than just human-intelligent teddy bears waiting to buddy up with people. They'd be elusive, mysterious, and still not very well understood. That being said, Legendaries would return to being spoken of only in myth and seen by people as a form of cryptozoology.
The characters would have to work hard and grow as people as they progressed along their respective tales, learning to battle and dealing with dangerous situations. We'd see more PG13 elements, possibly dealing with both violence and some romance. "Evil Gangs" would return to being gangs, rather than say...two individuals we see over and over. Gym leaders, the elite four, and other trainers would have lives and be out doing things rather than just sitting around waiting for people to kick down their door. The characters would occasionally have to prove themselves in order to line up a match, and earning a badge would still be a pretty big deal. No leader hands out a badge for free.
Battles wouldn't deviate much from what was seen in origins. Express a large range of pokemon abilities to be seen on screen, in use rather than just stick to explosions, beams, and tackles. There'd be no shyness about showing how brutal some moves could look, but there wouldn't be an excess of blood, if any at all. Pacing would be fast and intense, though matches would last a bit longer than what was seen in origins.
Music should be memorable and support scenes and setting.
>Also: Get rid of Ash