I think it would have been better if they had allowed a cross-side continuity with Kilian's army. The Nod Commander(the player) could choose between Kilian or the Loyalists of Kane.
The reason is that I am still doubtful about her. I didn't think she was behind the attack on Sarajevo Temple Prime. Ahay said that he assumed it was her he had no real proofs.
Actually it is revealed that Kilian was not a "real" traitor because all she wanted to do is "win" as she says when she proclaims herself Supreme leader of NOD replacing Kane. After her execution, Kane affirms and admits that he never intended to win the war against GDI and mentions that Kilian had found out.
Its sure Kilian Qatar was more respectful and a little more confident in winning next to Kane who just wanted to control an Alien Tower that may be clever but its ruthlessness for almost nothing because he lost several of his troops for nothing while his NOD operations were going well for world domination and GDI downfall. Kilian should of been head of the NOD new Order and Kane should have stayed in command of the original Brotherhood.
Although it is unclear if Kilian will return for a sequel. Ajay will however.
You know they can find a way to bring her back for the expansion: clones, cyborg face, ressurection or else.
For the expansion I'm sure they will bring back Jennifer Morrison and Grace Park(she didnt have a big role in TB Wars)
I don't think Gen. Granger and Director Boyle will return since there are two possible endings with these two so business is settled with them depending on which side the player chose.
Ajay might not return because he was out of business or executed for been disenfranchised. NOD will have a new A.I agent like a scrin. Kane will have a new military officer+ the player.
Scrin will have new commanders and warlords to invade Earth.
I think Kane was forcing Ajay to say YES to Kilian's possible betrayal.
Ajay hated Kilian Qatar but in the end he admitted that she must have been right since the beginning and that maybe Kane lost hs mind to Scrin domination.
What could have been an excellent idea would be to divide the last missions in two: 1- A path with Kilian Qatar 2- A path to follow Kane
In the epilogue we learn that Kilian Qatar is loyal to Kane the Messiah from the First and Second Tiberium War and THAT the actual Kane is a misguided clone commanded by CABAL the AI who survived the events of Firestorm.