Some random points on the P/R system (TL;DR warning):
-We may be underestimating the balance of the system, all things considered. It's worth remembering that a fair amount of renegade actions aren't really pragmatic, but straight-out sociopathic (the full renegade resolution to the Lorik Qui'in situation on Noveria comes to mind). This is probably because the system is as much an excrescence of the light side/dark side system of KOTOR as it is the idealism vs. pragmatism model it purports to be.
The balancing consideration, it seems to me, is that you can commit these actions with relative impunity. So it seems that just as a renegade can ask, "Why be renegade when paragon always gets results that are just as good?", the paragon can ask, "Why be paragon when I can unleash my id with near total impunity?" I would probably do away with the system altogether if it were up to me, but if the question is simply, "How balanced between paragon and renegade is the P/R system?", then I think we need to take a fuller account of the data.
-Two points on the endings and their relationship to the P/R system:
1. Looking at synthesis, intent clearly failed to translate into execution. Synthesis was probably intended as an option that, in broad strokes, is paragon in nature. But because it's offered by the bad guy (I doubt the developers intended us to see the Catalyst this way, but as the leader of the Reapers, he's bound to be seen as the bad guy), and because it involves unprecedented large scale physical changes to everyone without their awareness or agreement, it seems a lot more ethically questionable than intended.
2. Looking at the destroy ending in particular, I actually don't think that what bothers people about it is that it involves large scale sacrifice of friendly forces. Even a paragon might justify such an action on the basis of double effect or a similar doctrine. Rather, it's the racially specific nature of the required sacrifice. Here are two variations on Destroy to illustrate:
A. The crucible destroys the Reapers, but takes earth plus 90% of the fleet along with it.
B. The crucible destroys the Reapers, but selectively exterminates all members of [insert ethnic or religious minority group here].
From a numbers point of view, option (

is less bad than option A; after all, there are probably a lot fewer people in that group than there are people on earth, let alone earth plus the fleet. But if the Destroy option was set up like (

, you'd question the intentions of the writers in a way that you wouldn't with (A). Why are we picking on this one group? What kind of a message is being sent? It isn't just about sacrifice, because if you wanted a story about sacrifice you'd set up the scenario like (A).
The existing destroy scenario is a lot like (

, and I think that's what's behind the problems with it. By ME2, synthetics had seemingly become the game's take on the Other; synthetic/organic difference was a metaphor for cultural difference. From that point of view, the destroy option is bothersome more from a thematic perspective than from the perspective of purely in-universe ethical deliberation.