4 piston calipers will generally be always better than two, it allows for more even pressure on the pad surface. Bigger brakes will also be generally better unless they are a poor design. The only factor is weight, the bigger the rotor and the caliper the more weight. Personally I would tend to say that a big brake upgrade will be better. They may not stop the car faster but will last longer. Ie the 15th time you go to bring the car down from warp speed they will still be working far better than smaller brakes.
eg ss commodore vs GTs. 298mm twin piston caliper stop in like 40m from 100kmph. GTs stops in like with 362mm six piston caliper 39m but the GTS brakes basically never fade wheras by the end of one lap at a circuit the ss brakes are shot to bits.