It can be fun to do all of the story arcs in one run, though you will need to turn off xp at levels 10, 15, and 20 to complete all arcs and get the badges. You will out level Nova Praetoria contacts at 11, Imperial City at 16, and Neutropolis at 21 so plan accordingly. There are a few gotchas you need to be aware of first as some contacts will be removed from the game depending on what missions you do. Review the guide posted above and you will be fine. Also, I find having some form of stealth is beneficial for most of the missions. Alternatively, you can just run by all the yard trash as they (mostly) do not follow. Some missions however have ambushes that will continue to spawn and follow you anywhere, even through elevators. If you find things are too tough, you can always set difficulty to -1.