I assume that you would need to pay to enter and leave towns, considering there is a guard at every important scenery change. This makes even more sense considering that they don't own houses or pay taxes. There would be places like hotels or inns on routes, I don't think it would be like the anime where EVERYONE camps outside.
I'd imagine that you would need a permit to surf or fly, you're permit could be the HM itself. This leads on to eventually having a permit for all moves being used outside of battle.
There could be a ban or even extermination on certain Pokemon that instinctively harm others or the enviroment; I can easily imagine the Koffing family or the Grimer family falling into this category. Legendaries would be captured and tested on by the goverment, not only secret teams like Team Rocket and Galactic. But legendaries would be powerfull and I mean POWERFULL.
Crime would be off the scale, everyone would need to have Pokemon to act as protection or guards. Pokemon would be used in crimes such as robberies or mass murder.
I also would like to think if Pokemon are capable of undertsading humans and can obey their demands. By the fact that legendaries don't attack humans must mean that they want to live in peace. This could lead to cataclysmic or paradise. As long as humans don't get too crazy with controll and power I can imagine the Pokemon world being quite happy. However if the goverment do try and get taxes and scams on everything it coulod easily turn bad.
Mystery Dungeon Blue/Red team explains this perfectly.