Does Natural Aptitude: Piloting apply to physical attack rolls? They use the Piloting Skill, but are they true piloting rolls?
Natural Aptitude applies to any use of the related Skill.
If yes, I'd absolutely go for the 4 NA/5 NA over the 3/4.
Yep, it's massively better. Crudely speaking, it can be looked at as a +2.25-ish bonus, though it's a little different. You can still roll three 1's, while an actual +2 bonus would make a result of anything less than a "4" impossible, ignoring modifiers.
Edit: Forgot to include: Of course, it does help some with uAC/RAC jams, and MASC/supercharger failures, since those events don't look at modifiers, they look at what the dice end up being, and you're far less likely to find three 1s (so you resolve to a 2+1 result, avoiding failures) than you are to find two 1s.
Good thing the skill doesn't apply to crit rolls, or possibly even more powerful, to-hit rolls. On three dice, you can arrive at 3 different hit locations (thus picking the ones that will hurt the most), while 2's and 12's become much more common end results as well.
Now, 3/4 vs 4/5 with *only* Nat/App Gunnery, and nothing on the Piloting end, that might be worth a moment of consideration, but I'd likely still take that. Unless my Mech was heavily invested in physical attacks.
Paul