Of all the suggestions you made, this is the one i like the most.
That being said, its difficult to replace Vermillion as main hub as that city is populated based on the fact that its the bridge between both regions. So unless there is some "unique" attractive in the new city, it will pretty much get lost in the map. And the devs consider cost/benefit when implementing something so there is little chance of this happening. The other major con i see is that making it "post game only" is kind of elitist.
Cons aside, i can only dream of some flashy 4gen+ graphics and sakura/leaves/snow animations that make it possible to drag players just for the aesthetics. Then again, not likely gona happen.
etc