I did like ME letting you gain points in both meters, because not being a saint in every situation does not somehow permanently taint your personality...
But the meta-problem with it was taking most of the big Renegade choices genuinely ended up sabotaging your war efforts in the long run. There wasn't an interesting trade-off to killing Wrex, you just got a more pissed off and uncontrolled Wrex-analog who would backstab you regardless.
As mentioned, being kind of a dick in AP was the only way to make a few people co-operate with you, and DID gain you tangible benefits at times, but only if you knew enough about which people to poke the right buttons to make it happen.
ME was still way ahead of the childish duality in most Star Wars games (bluh), but in the end it still lapsed far into didactic parables that soured Renegade paths in a big way for me.
The only other plots I can think of offhand that offer the same level of choice come from Fallout. As much as I despise FO3's teen power fantasy, The Pitt DLC was fantastic about its moral dilemma. Most people immediately side with the slaves, but doing so may very well cost civilization in the future a priceless working foundry AND potential medical breakthroughs. Let's face it, there's no way at all Werhner and crew could have done jack shit by tormenting that baby, if they even intended to try (I don't think he had any intention of doing anything besides becoming the next slave driver). Morality should be about tough choices, at least sometimes, with no black and white answers. Life is complicated like that.