The original cyborgs are said to be made by mutants and prisoners (experiment subjects), so implants are there in case they go rogue, which did CABAL a huge favor when he needed an army.
There were slight implications of CABAL's own ambition during his tactical AI duty in TS, such as this quote from the Nod mission 3B (rescue an Hassan's former commander): "The commander may have information vital to my... your movement."
The Nod ending of FS indicates CABAL and Kane share the same pattern of thinking, and it is not for the best interest of mankind (apparently), which reinforced the TS Nod ending, and it could be Kane's own attempt to achieve that goal in another way.
The reason CABAL eliminating the Inner Circle can be very simple, he needs to come into power. Also Brotherhood won't funtion well in the hands of these warlords, even at Slavik's best effort he failed to control them, and Kane didn't trust Slavik enough to reveal his real agenda or real shape, so he had no choice to forsake the unusable human army at the moment, (when he can't come out to lead the public) dispite the CABAL army wasn't mature.
CCR somewhat explains that Kane's plan on human, in the name of "Divination", is turning human into species that can survive Tiberium environment. It's the root of mutants, but there are some differences with cyborg army, for one thing cyborgs are unlikely to reproduce, so unless it's but halfway to pure robot army, killing off everyone may not be a good idea.
Ascension is just a typical bad ending when the writer have no clue where the character is going.