If the world of Shadowrun is (partially) re-emerged and its nature is re-vitalized -- vast forests regrown, magic returned, etc --, why would the setting's megaplexes be as super-polluted, over-populated and "ersatz-dependent" as the cities of other (oldschool?) cyberpunk works, where nature has practically been 100% ruined?
There are several reasons
In a cyberpunk world, cities are overpopulated because people have little reason to live outside of cities. The reasons are varied but are somewhat connected, so I will try to briefly go through some of them:
Humankind is strong because we are legion... I mean, because we are many. The other races are prejudiced because they are fewer. You think orcs and trolls had a hard time? Check the sasquatch, centaurs and fairies, they don't even get to be recognized as people, the governs classifies them as sentient animals. That means no citzenship cards, no jobs, no food, they can't even vote because they are less than 1% of the relevant population.
Humans still rule the world (most of it, anyway), and even the strongest publicly known threat, dragons, have fallen against mankind's weapons. Yes, there are countries and cities ruled by dragons, spirits, insects, elves, etc. Lots of them, but those are not the norm, they are exceptions.
This goes beyond the game, it's historically accurate. Small villages were easily wiped out by groups of bandits. Larger towns were easily conquered by a small army. Those with more soldiers usually beat those with fewer. A lot has changed since we last wielded swords and spears, but the concept remains the same. Alone we perish, together we endure.
Everything can be found in cities, everything. And I am not trying to sell you anything. From weapons to soldiers, you can find and buy things in the black markets that would not be available otherwise. Not only that, cities have information, and the information is power in the sixth world.
Maybe your average Joe could care less about being educated, but he certainly loves all the movies, novels, comics, music, chats and connections for his hobbies that he gains by being a member of a large city. Especially when we factor that people can nearly live inside the Matrix of the sixth world. There are stories of people who forgot to eat because their virtual lives were more interesting than their real lives.
Do you need your periodic fix? Search on the matrix and you will have it delivered home. Need medicine? You can buy from clandestine doctors. Need the latest video of someone being tortured by Japanese mafia? Well, that's difficult and will cost you a month of your wage, but it's totally worth it if you are into that... Creep.
As long as you have money, information, or connections, you will have anything you want in the sixth world.
Forests and wild areas in the sixth world are not safe. Along with magic, several new paracritters now are back into the world, from fire breathing wolves to man-bears that eat human flesh. The wilds are not safe. There is a published adventure where farmers had to hire runners so they would get rid of certain sentient creatures that were attacking people at night and devouring their cattle.
Fun fact: Even the forests of Amazonia are dangerous now, people hide behind extremely large walls so they are not literally attacked by trees. The forest is alive now, it has spread uncontrolled and reached nearly all of South America.
The Shadowrun Sixth World Almanac is a really strong book about understanting the setting. It goes into details about the timeline and current situation all around the world. It contains reports of smaller cities that are barely putting it together, located on the poorer corners of the sixth world, where matrix access barely exists and medical attention is nil.
People there suffer. Not because of banditry or paracritters, but because nobody wants to even look at them, they are being ignored by society. Why would corporations bother with a small village of 200 people located... Where was it again...? Ah, forget it, nobody knows where without the help of a map. Not even public relations would benefit from it.
Even if you do get some glimpse of attention, it's usually to promote some new president of a small group, or a new celebrity, for the small percentage of the voters/buyers who still care. Normally it's to divert attentions from elsewhere, don't worry, it won't last long.