My ideal Pokemon stage would have to be...Route 1. Well, I guess it doesn't have to be that specific route, so long as it follows the same basic idea:
1. A scrolling stage, slower than Mushroomy Kingdom, but in the same direction.
2. BIG (like Bridge of Eldin-sized).
Of course, there'd be patches of tall grass every now and then, and random wild Pokemon would attack you if you walked in front of it (it wouldn't actually be on the stage, so as not to obstruct vision). There'd be lots of variation in the elevation, with those little "jump cliffs" being represented as organic hills you'd climb up. There could be sections of shallow water (marshes) or deeper water (rivers, lakes), a desert area, and so on. In this way, you could display all the different kinds of Pokemon (maybe you could even take a short trip through Moon Mountain, and if you wanted to see more than slightly ahead of you, you'd have to attack a Clefairy to make it use Flash). Of course, in the background, there'd be all kinds of scenery--trainer battles, people on bikes, and even entire towns in the background.
...
Basically, a stage that represents the entire world of Pokemon!