Putting aside whether there were always logical consequences to paragon choices, a fair amount of renegade choices were pretty terrible and should have had poor consequences attached to them. The problem as I saw it wasn't that renegades were punished so much as Paragons were insulated. Generally speaking, Renegade choices were pretty antisocial.
I've always viewed the way "bad" and "good" outcomes to be presented in most games (not just Bioware games) to be a real dichotomy. I liken it to Risk Management - which it basically is, since the player is making a choice with limited information on what the outcomes or results will be in most cases.
Choosing "good" I would view as a pure positive risk, which is to say that only two outcomes happen - something good happens (relative to the other choices) or nothing happens (again, relative to the other choices).
Choosing "bad," on the other hand, i would view as pure negative risk, which is to say only two outcomes happen - something bad happens or nothing happens (again, relative to the other choices).
To demonstrate, let me use the most infamous of choice outcomes, ME3's Rachni Queen. Regardless of your choices in previous ME games, the Rachni Queen is turned into a monstrosity by the Reapers, which you encounter in ME3. And again, regardless of prior game decisions, you are only given two choices - kill the new monster Queen or free her.
The ME1 Paragon choice of letting the Queen escape results in two outcomes - you kill the new monster Queen (Krogan special forces added to your War Assets) or you set her free, where she turns into a War Asset for you, helping your cause.
The ME1 Renegade choice of killing the Queen results in two outcomes - kill the cloned queen since you killed the first (again, earning you Krogan special forces) or set her free, where she turns into a War Asset for you, helping your cause... for a little while. But then the Queen turns rogue and kills part of the research team working on the Crucible, resulting in a War Assets LOSS.
Hence, only neutral or good results came out of Paragon. And only neutral or negative results came out of Renegade. That's not good design.
One would hope an equal (and logical) balancing of outcomes between the two would be present. Not in every instance, but at least in some. Although, ideally, removing a clearly labeled morality choice would be better. Saving the Anvil in DA:O would undoubtedly have been labeled as a Renegade choice (ironically enough, titled Paragon of Her Kind), but I think giving the dwarves a fighting chance against an ever-encroaching Darkspawn horde is choosing the greater good. I don't do it for the evil-lolz or selfish power reasons... I do it because I truly believe it is the best chance at ensuring an entire race's survival. I'm not being "edgy" or "power-hungry" or anything normally attributed to "bad" morality, but such a shallow morality system would have my choice labeled that way, regardless.