So one of the things I have always wanted since watching the anime of Pokemon when I was little, was in the games to have interactions/battles with Pokemon inside the city, just like how there are wild Pokemon inside the cities of the anime. I thought a cool way to do this would be to add in little alleyways behind buildings in large cities, and have trash cans/dumpsters and other items that would shake (just like the grass) when a Pokemon is in there. I thought that it would be cool if Grimers/Muks and other Pokemon that are repeatedly shown in the cities could be the Pokemon that could be encountered. I think this could be an awesome new encountering method that could be installed in newer Pokemon games, like Pokemon X & Y.
I actually like this idea alot. I mean, why just have Poke's in the grass outside of cities? We could find Grimers/Muks or Garbadors/Trubbish in trash cans, if we can go ontop of buildings, then we could find flying types. Stuff like that would be cool to have in X and Y.
It's a different way of encountering new and rare Pokemon as compared to the traditional method and adds an element of excitement, I think.
As to the possibility of encountering Pokemon in the overworld via interaction, I've been wanting this for a long time. Especially with larger Pokemon like Onix or Aggron. Maybe it'd be like encountering a Trainer, with a Pokemon noticing you and giving chase, giving you the option to battle it or run before it makes contact.