Warning: Taking the below too seriously may cause an increase in blood pressure.
Shadowrun is a dystopia: It's over. Metahumans in Shadowrun have more rights than many people today. The lowest exploited are meta-sapients and people are even fighting for their rights. Even ghouls have rights now and AIs are getting SINs in the 2070s. It's easier to deal with the MDC checkpoint in New York than to deal with TSA to fly to GenCon in 2011. The dystopia is over, please return to your homes and watch Tri-D.
People are afraid of Magic: Again, over. They're employees now, with stock options. They walk right through the millimeter wave radar because they don't have to carry a gun or be wired up. If anything, people are jealous of magic because it means job security, freedom to walk the streets tonight, and a good enough income to have a private seat at the club.
Seedy Fixers: That was a generation ago. If you want plausible deniability, then you need to go through professionals. Why fixers don't appear to work like the companies in "The Mechanic" or "Mr. & Mrs. Smith" and instead are Street Thugs like you find in this season of Missions is beyond me. This isn't the Wild West anymore. If you have a specific job with unusual requirements you hire a discrete contracting firm who can assemble a team for you to do the job.
Soy Food: There is plenty of good food. Even the first story in the SR4 book has a fishing boat (and you can buy one in Arsenal). Runner's Companion has piles of great food in their lifestyles section. Sure, the gangers are eating soy, but chances are you're on the top of the food chain because you have the ware, the contacts, and you're hanging out with mages, any one of whom could be pulling in stock options right now. And if you are a mage and eating soy we really need to talk about life decisions.