Ok, as I was reading your stuff, I instantly backtracked to a game idea of my own, and I have no qualms with you using it, just so long as I don't get sued for using it in later games if this game goes well, lol, just kidding.
Have you ever played Amazon Trail? It is a sister game to Oregon Trail. In it, you travel down the Amazon River learning about the nature and the history and the animals in it. It was amazing, and far better than the successful Oregon Trail.
The reason I am bringing it up, is that the game had a feature where you could move to a screenshot to take photos of wild-life, collect fruits and berries, and learn about the wildlife. We could include this as well, where the player doesn't need to battle Pokemon to get them on the Pokedex. The player could snap a photo of them using the camera app on the Pokedex. You could also have a Print app that lets you keep the photos in real-life, though that bit is a tad out there. This method would give people a more passive way of learning about Pokemon, without battling them. You can also use bait and rocks without being in the Safari zone, this is to provide a more open and controllable feel. Coax them with bait and avoid battling all together. Or maybe you want to scare off a Pokemon you don't want to deal with in battle.