"And we both become as kells, yes?"

The queen very openly sent us to what she believed was certain death to the Gate Lord. Keep that in mind. Variks had his arms docked by Skolas. He could've killed him, but he didn't, he shamed him and allowed him to live. Skolas fought to be Kell. As we know, fallen are seemingly natural aggressors, and to be Kell certainly means dirty work. That doesn't make him our enemy. Skolas goal was to unite a shattered race. No mention of "to kill guardians, to rule the cosmos, to attack the last city..." etc. The 9 let Skolas go after he was captured by the queen, who tried to kill you. He was captured for what Variks, the guy he shamed, told the queen Skolas was planning. This information is 99% bias. Skolas' people are systematically assassinated by guardians based on information attained by 1) a queen that hates guardians, and Skolas 2) a shamed traitor that hates the queen, the guardians, and Skolas. At Skolas last bid to save his people using vex portals, we are sent not to kill, but to capture. We are then sent to a prison to literally kill the inmates without cause. During this process, Variks attempts to kill the players on numerous occasions by placing lethal objectives on their path, with an unheard of two attempts at Skolas. Variks collects ether seeds, which grow fallen, and elder cipher, a secret code we are not privy to once it's unlocked. Seemingly neither is the queen. To quote Colonel Kurtz " You're an errand boy, sent by grocery clerks, to collect a bill."

He is collecting elder ciphers, and it's directly stated that they allow control to ether flow. If he has ck tell if ether flow he'll be able to become big enough to be a kell(maybe even grow back his arms if possible?) so that enough can give us a hint that he's trying to regain control of the fallen, or maybe just trying to rebuild his house since it was lost in his species collapse.

He is a fallen Elinksi (idk if that's how you spell it) it's in his nature to be a klepto. Fallen are essentially pirates and Variks loves booty

Well, yeah, Variks is naturally going to be most loyal to his Fallen house. However, we also know that House Judgement is in a state of disrepair right now. Variks probably wants to rebuild House Judgement and bring the rest of the Fallen Houses back into order. My favorite Variks line is, "Does the great machine speak to you, as it once spoke to me?" implying that Variks once held the position of the Traveler's Speaker to the Fallen.