I think in terms of exploring grey morality, it's nice to have Rufus as a complex, nuanced character who does bad things for what he believes are the right reasons instead of just a wholly irredeemable Joffrey type brat. Make no mistake, he can be a little shit, even more so in BC than in the original game (I may or may not have yelled at my screening while watching play throughs and wanted Tseng or someone to punch him), but I like that he's also complex because it fits with the overall exploration of good and evil.
I'd be more okay with Rufus presenting a more nuanced not-quite villain in the compilation if the same characterization didn't apply to every other villain in the compilation. Every villain has some kinda of tragic story behind them that makes them do what they do, Deepground are these forgotten experiments buried underground who come to the surface thinking they need to purge the Planet and basically start afresh through Omega, Genesis is the victim of experimentation that wasn't as succesful as his rival's, the original AVALANCHE are the rebels who commit atrocities in the name of saving the world. Having so many tragic, pseudo-complex villains dilutes the effectiveness of Rufus' and Shinra Company's role as the morally grey characters, IMO. It makes them just another in a long line of morally grey villains in the compilation who we can't quite bring ourselves to label as villains.
What the OG did well was explore the moral grey areas, as you pointed out, but still provided an absolute evil that was necessary to overcome. You were the heroes caught between two evils. Shinra, who would, had they succeeded in their plans for Neo-Midgar, benefited numerous people, but that was more of a side consequence of their main goal which was to extend their own power and profit. I don't buy into Shinra wanting to do things for what they see as the right reasons, whatever way you cut it, dropping the plate on countless civilians just to get rid of a small group of rebels isn't morally justifiable and was purely a political power play and Rufus blithely admits he wants to rule through fear and tries to execute people just to protect his own interests rather than out of any moral indignation with Avalanche. The reason they turn against Sephiroth is because he's a competitor trying to achieve the same goal as them, total dominion and power, he's just going about it differently and his succeeding would obviously be detrimental to them.
Then you had Sephiroth, the other evil, who we could sympathise with to a much greater extent because we can understand how horrifying it was for him to discover the circumstances of his creation. But once he comes back, he basically divorces himself from that tragedy in favour of pursuing power, of becoming a God and ruling over all. Thus we lose our sympathy for him and he comes another absolute evil that must be stopped.
Then there's the heroes, who have done morally reprehensible things too, but who are also somewhat self-interested, insofar as Cloud mostly fights to settle the score with Sephiroth for the evils he has done, or Barret mostly fights to protect Marlene. But they also have a compassion for others, they go out of their way to help Aerith when she is captured, they go with Red into the Cave of the Gi even though it doesn't really benefit them at all, it's things like that which make us identify them as more good in their moral greyness than evil, like Shinra, or absolutely evil, like Sephiroth. And ultimately they have no choice but to try and take on Sephiroth and Shinra, as should either succeed they will be killed, subjugated and tyrannised and their home, their planet will suffer.
I've ranted a bit too much, but basically I think the OG did a much better job of subtly exploring moral grey areas and making you think and feel whilst still providing an absolute evil to overcome than a lot of the compilation titles did. The compilation has become
too morally grey...as well as just grey in general, damn colour pallette. So characters like Rufus who are trying to redeem themselves have our sympathies and desire to see them succeed diluted, because there's always other people we have to devote that energy to as well, most of them the central villain of the piece. Sure there's always Sephiroth, but he wasn't much more than a footnote in Advent Children.
Does that make sense? O_o