Essentials has the physical/special split by default - it just doesn't show it. Try using Surf and Waterfall on a Blissey or something - you'll notice Waterfall does more damage, even though it has less power.
This project is looking outstanding. You've got a high quality of mapping which is making the world look like a real Pokémon game - you're using tiles correctly rather than just shoving them in any old way! It sounds and looks interesting and enjoyable.
Your menus have been put together very well and the region map is looking very good indeed ;)
We've seen a lot of screens now, so try not to show off TOO much of the game dialogue for the moment - but keep us posted with new features and stuff! It's gonna be a big success and the high quality speaks for itself. Keep it up!