It will be a key item obviously. Also, a bike will be faster than running shoes so there is still reason to buy a bike. I'm also thinking of cutting off bits of Johto which i'm sure some people wouldnt want to visit again e.g. Radio Tower, Team Rocket Hideout, Milkman's house and so on. Here is a list of what im keeping, adding and losing:
Keeping:
All major routes and towns
Lake of Rage (yes, after some thought im keeping it, that doesnt mean it's gonna be the same though)
Bike Shop
Ilex Forest
Huge pokemart
Pokemon school
Sudowoodo event (its in a different place though hehe)
Union Cave
Losing:
Mt Silver
Bellsprout Tower
Milkman's farm
S.S.Aqua
National Park (don't worry you park fans, check what im adding)
Radio Tower
Team Rocket hideout
Dark Cave
Mr. Pokemon's house
Adding:
Battle Halls
Battle Garden (similar to National Park, just a shiny new name and venue)
Cave leading to (drumrole) Rijon Leugue!!!
Underwater Cave
Running Shoes shop
Skatepark (this is pending, it may be removed)
Hotels
Long list eh? Any questions please ask.