Stock EEC with a tune will work great for most cars. We tuned a street driven Turbo Gen 2 Lightning that made 800/800 last summer - stock EEC with a tune.
I think the main question is do you want to tune yourself or have someone tune your car? If the answer is the latter than either will work, just have a reputable tuner use either the PMS or SCT. But down the line if you want to tune yourself the PMS will be nice or you will need the SCT Pro Racer Package.