I don't have alot of experience running games that allow for as much planning as Shadowrun does, and it's this change in style I'm having issues developing challenges for. My current college group is pretty green to tabletop rpgs in general so roleplaying encounters are pretty quick and straightforward for the time being. And I have a good hunch that the system (and your standard SR player) doesn't take kindly to a 'dungeon'.
It's just an alien concept to me to have an element in the scene that can and is actively trying to murder the whole team in violent fashion after years of D&D with my family that amounted to "everything that can be killed in this fortress/mine/palace/desert should be killed"
So what can I do to create an environment that needs work to be done before the hit? How can I make it dangerous but give an advantage for a good job done on recon?
Some ideas I've had determining guard shifts and making it just overwhelming to sneak in while they're on full duty or drawing up alarm drones that are bad mofos to run away from rather than fight head on.