Politics are as good as any other reason. My first character, an Argonian, joined the Stormcloaks and while he didn't approve of some of their methods (mainly the racist ones) it would be quite the hypocrisy if he was willing to die to defend Argonia's independence but not Skyrim's. The Empire was more corrupt to him and the very thought of them lying in bed with the Thalmor made it worse. Knowing about the racism that flowed in Cyrodiil also shines bad light at the Empire, especially when they try to hide it from public knowledge. Not to mention that the Empire made it personal when they almost wrongfully executed him and later his lover, then murdered a very close friend, desecrating the body in the process.
The Hist are a dangerous threat and the oldest being on Tamriel I am curious to see what would happen if somebody were to invade Black Marsh now thay would surely be a spectacle.
Even more so since the last major event Argonia suffered was 160 years ago. The Great War was 30 years ago. IIRC elves aren't the most productive breeders and since Argonians have had more than a five times longer time span than the Thalmor to rebuild their military, the two factions have at the very least even military power.
Under Hist influence, the daedra were forced to close the Oblivion gates themselves because of the Argonians' ferocity. The elves didn't fare as well as the Argonians. So Argonians under Hist influence are quite the threat.
EDIT: And to my knowledge, no faction has ever truly conquered Argonia. Not even Tiber Septim or Reman II succeeded. The inner swamplands near Helstrom has always been Argonian.