Varis' primary concern appears to be finding some way to put an end to the Eikon threat once and for all. His reasoning for this, in his words, is due to how they threaten the very life of the 'Star' - which refers to Hydaelyn itself. This, at least, aligns with the goal of the Warrior of Light and many of his allies. Elidibus whispering in Varis' ears is an additional complication, certainly, though given that Varis is supposedly a master tactician it isn't unreasonable to assume that he wishes to explore multiple options.
The Ambassador being Yotsuyu's cousin is an additional complication. Could she, after regaining her memories, snap and take him out in a fit of rage? That would certainly complicate things - especially if he genuinely approached with pure intentions. Is he the same individual standing in the throne room and clenching his fist? I have my doubts, since it's likely he is largely based in the Far East.
I cannot help but note that there is a brief scene in the trailer where the Warrior of Light is crouching down and another figure clad in armour from head to toe approaches him. Is that the figure from the throne room, perhaps? Someone who genuinely wants to warn the Warrior of Light that there is trouble brewing in their homeland.
As far as distrust towards Garlemald is concerned, I feel like a lot of it is based around key characters simply not understanding Garlemald's situation or its history. Let's not forget that they themselves have had most of their recent problems solved by the convenient 'quick fix' that is the Warrior of Light. Not everybody has had that luxury, thus their methods to deal with issues have differed. Garlemald's story is, ultimately, going to have to lead to Pureblood Garleans being free of persecution based on their inability to wield aether...as well as an adjustment to Garlemald's foreign policy. As always, it comes down to nuances.
As a random aside, I can't help but wonder if the bosses in Omega are influenced by Nero having meddled with Omega back when it was stationed in Carteneau. After all, I believe at least one of the first bosses was associated with a Garlean tale. The Phantom Train and Kefka seem like they would be prime candidates to also fit Garlean tales, too.