Short answer is FI M54.
All kits are going to give you better usable power (low end torque) compared to stock S54.
I happen to be a big fan of twinscrew design. While the dyno numbers might not be as high as centrifugal SC or turbos the throttle response and torque is worth the extra money.
The S54 will only make sense if you ever want to take your car over 350whp.