Did a little bit of digging in the game's graphics, and I found some pretty neat stuff.
The name of this sprite is Professor Holly, who doesn't make any appearance in-game. It's not Professor Cyrpress' (I double checked), so I guess they were originally going to have four professors. UPDATE: Found a sprite that goes with it, but her name is Professor Lily, so it's hard to tell what was going to be her name.
Sprites for some of the EV ninjas. I could only find three, so I guess this was scrapped and left as just regular ninjas. Tarou's sprite explains his comment of "I'm in shape-round is a shape!", though.
According to this file's name, this is supposed to be a sprite for JV. I imagine that they were planning a "meet the team" event like the main series games have. Looks like this was cancelled, too, there's no sprite I could find for Twitch.
Maybe it's just me, but I don't remember seeing any of these Pokemon in the overworld. Obviously starters could end up being important, but the rest make me curious as to what they were going to be used for.
Hey, it's the game's icon!
My guess is that this is either an early Nuclear Ball or what was going to be the Atom Ball. (mentioned when Urayne joins the player) Either way, looks like it was never finished-no summary or throwing sprites for it, just the item.