Hi DevianID - In our games we frequently play with mechs that have 5+ damage. So, the core rule of rolling 5 separate attack/damage rolls really slows down the game. It's not unusual for us to have 9 damage - and rolling 9 separate attack/damage rolls is just not realistic.
The Pilot Die, on the other hand, I can just pick up all the dice and roll them at once, with just a single differently colored die. So, in the 9-damage example, I just pick up 10 dice, roll them all at once, and quickly determine how many hit. And switching between two different approaches depending upon whether a mech is doing 3 damage or 9 damage seems confusing and cumbersome. So, IMO, the pilot die approach works very well for any damage amount, whereas the core rule only works when the damage is lowl
In my personal opinion, there is really no comparison in terms of ease of play between the two systems.