Be not afraid to custom-build the NPCs that oppose the PCs. I did this last night with my Feng Shui, and the resulting fight was the scariest thing that the PCs encountered to date.
(Note: The NPCs were Abominations, using the template in the rulebook, based off the Zaku II F/J from Mobile Suit Gundam. I increased their Body scores by one to 11, added one additional Creature Power schtick and one Stat schtick on top of what the template provides. I equipped two of them with Hellharrower 9.62 mm battle rifles and the last with a homebrewed bazooka: the Buro Demonfist (holds a five-rocket magazine of Woodchuck 70mm rockets).)
Be not afraid to adjust published NPCs, either to account for the gear that they should have (but wasn't noted) or to properly give the PCs a stiff challenge.
(Note: Seeds of the New Flesh is the supplement for the 2056 juncture, where the world is a global dystopian facist police state. The formost cop is a Judge Dredd ripoff called Dan Dammer, so I ran with the concept and gave Dan a Lawgiver and a Lawmaster. He and his Lawmaster forced four of the five PCs to engage him in order for the PCs to achieve their objective and get away. Damned potent stuff.)
Be not afraid for actions to have consequences. The PCs last night killed both of the NPCs that could've gotten them to their objective and out of hostile territory without incident without trying very hard to suss out who those NPCs were or what they knew. So they got into a fight that wasn't necessary and nearly got killed on the way out.