It's pretty common for a majority of enemies to be pretty weak compared to the party.
1. Remember, the players are often not trying to go slay some character in their lair like some other game systems. (Although that does happen sometimes) Their goal is to beat a security system usually, and in many cases killing can actually hinder them. (The more bodies dropped, the more chance they are found and alarms go off, similar to killing IC in the Matrix and more alarms going off) A complicated architecture for a site and a bunch of weak guards can actually be worse than a single room with highly elite guards....because alarms may go off and elite response forces and police will come.
2. This is also a game where if you try to perfectlly balance encounters like you do in some other game systems you run a high chance of killing players. It's a lethal system.
3. There is absolutely no risk in making enemies too weak. All that happens is they die and the game goes on to the next scenario. The risk of making them too powerful is much higher, especially if the game has been around a while and PCs are attached to their characters. (And the GM is attached to his scenarios/story playing out) If you weren't happy about how weak your enemies were last session, you can increase em a bit next session.
4, It of course depends on what is being guarded. Elite cyber zombies are not going to be guarding the local Nukit burger manager's office. They very well might be guarding the Weapons World Exec the players are trying to assassinate, along with a clutch of powerful fire elementals.
Personally, I like a high percentage of weak enemies these days. Then it's a real shock when the players do run into equal forces, say when they run into an opposing Shadowrunner team or an elite military strike team. I was an old AD&D DM and I got into alot of trouble with trying to run Shadowrun like that as far as making challenging encounters where the PCs are just on the borderline of losing.
Of course if the players do stupid stuff like hang around target sites too long then they definitely should run into forces their equal and greater. They're asking for it, bit off moe than they could chew, or they made grevious mistakes at that point.
