Interesting thoughts.
I agree that the ballistics system could be used for more, but it has many advantages vs rolls. For example, consider the body part targeting. Unlike in the original fallouts, in PP shots that miss the intended body part can hit the target elsewhere, or hit something else. Also shooting at a destructible wall to hit an enemy behind it - you can’t really do so well with die rolls. Or using an auto weapon to hit multiple targets (something that is underutilized in PP, TBH).
Yes, you can use some mechanics with die rolls to get around these things, but you can’t replace something like discretely moving around the aiming reticle to choose exactly where to shoot and the projectiles behaving in exactly the same manner whether you are aiming at an enemy, a friendly, an object, or nothing.
My view is that using die rolls to determine to hit chances has many advantages, but the big disadvantage is that all you are doing is rolling dice. With ballistics, even if very simple, like in PP, you get to do something different (or at least I feel this way, other players might not - @SpiteAndMalice for example doesn’t see any difference given that the exact trajectory of the projectiles is determined by die rolls and the characters are static, so basically the die roll that determines the trajectory is exactly the same as the die roll that determines the to hit chances, but with unnecessary obfuscation).
As to the skills, I think PP could have easily gone with a different approach regardless of the ballistics mechanics. For example, there could have been skills to buff accuracy, or damage subject to particular conditions. Or there could be a penalty to accuracy from movement, and skills to reduce this penalty under specific circumstances.
However, as someone else (@Wenlock) has put it, PP is a wide open tactics game. So I would say that many of the skills in PP subvert the core systems, rather than bypassing them. This is not bad in principle (unless you want a more classic tactics turn based game), at the moment it’s just too much.
But when everything works, it works really well. Chirons, for example. They are great, actually (double explosion and the acid mess aside). They are a control on the player who is careless about detection, like the sirens are a control on a player who is careless about overextending. However, you have a situation where this is not explained to the player and where at the same time the player is given enough tools to end most missions on the first turn. Result: most players are oblivious to the existence of the detection mechanics except insofar as it concerns infiltrators, assume that the only reliable way of dealing with Chirons is killing them on the first turn, for which they need to use OP tactics, which are basically exploits.