3) How do you (I'm looking at you experienced players/Gm's) design your basic enemy goons? Do you simply copy the book templates as is with minor alterations or do you have some system to randomize a little this step? I've thought about counting attribute and skill points of every PR level and then just moving them freely but I'm not sure that's the correct way to do it.
I almost never get as detailed as writing out a complete stat block. At most, my goons will have 1 physical attribute and 1 mental attribute, an attack pool of dice, and a defense pool of dice. I completely fudge these numbers, I just assign them based on the difficulty they're supposed to represent.
I use a dice pool of 12 to represent opposition equivalent to a player character in their specialty. These are pro's.
10 represents well trained opposition.
8 represents basic competent opposition.
6 represents poorly trained opposition.
Less than 6 is non-skilled and normally not worth rolling unless the story would be better for it.
Dice pools higher than 12 are the really dangerous NPCs that have a chance at defeating the players.
A typical encounter I make that is meant to be challenging will have a group 1.5x to 2x the number of PCs with attack dice pools of 8. 8 is a normal defense pool that non-combat specialist PCs tend to have, and they will occasionally get hit.
Dice pools are the main thing, but then you add in flavoring:
Special abilities. anything beyond your basic gun, that means these people have grenades, or a flamethrower, or are immune to fire damage because of their armor, or use stick n' shock ammo. I just pick 1-2 things that spice up the encounter.
Specialists. Your team will probably come to an encounter with a combat specialist, a mage, and a decker, attacking on all three fronts. When you mix matrix or magic opposition to your group, you make encounters a lot more tactical. Especially when you hide these elements and ensure they survive a PC alpha strike.