After reading through the full compilation's timeline, it seems evident that they have tried to fit way too much into the world of Final Fantasy VII.

(SPOILER)You have the issues with the Cetra and Jenova; Jenova S (involving Vincent and Lucrecia) and G projects ( involving Genesis and Angeal); the original AVALANCHE being bat crazier than Shinra; Rufus trying to kill his father and conspiring with AVALANCHE to achieve that; Shinra's Deepground experiments; Chaos and Omega; and I'm sure there's more I'm missing.

They're just trying to shove too much in there, and I'm sure they could rewrite the whole compilation including the original to be a much more coherant and better telling story.

Oh, and if you play Before Crisis you'll notice that in general the Turks have a great sense of compassion. (SPOILER)Tseng gets himself into trouble quite a bit due to that, and only made it as the leader of the Turks because he was forced to execute Veld in order to save the rest of the Turks' butts. So while in the original game they tried to write them as being ruthless, I think their compassion that's been expanded on during the compilation really shows a nicer side to them.