well mr mc happens to be married 1 of alien leader's daughter and had kids with other and is supreme general on other so there shouldn't be problems on getting terraformi engines or smallish planet which is habitable for humans but not to aliens but your game so your decision.
Ezan is just an ambassador, not a leader, while he does have some weight behind his name he isn't really involved in the high-end decision making. Changing the research treaties served Elai Republic, as does the location of the Sentinel for trade. Ot'ai only cared for the psionics on the station, and the only reason they really agreed for changing the treaty was the psionics on the station could be "healed" and freed.
And as far as the title goes, it's honorary, it's even stated in the game I believe. It is the highest honor the Kraed Empire can give to non-Kraed for saving an heir to the throne, one of them anyway. Sure, any soldier would obey Garrett's command in a battle, as long as there wouldn't be anyone higher of their kind present, but that's highly unlikely.
Naelea is also just an ambassador, and she had the children for her own selfish reasons. The only one who you could consider leader is Qivian, but that's because she is Elder Matriarch which translates that she leads a clan that rules an entire system, and the clan matriarchs decide what is "best" action for the species. Most of them aren't going to help male-dominant species, simply out of principle.
The story in this game isn't the first one in this setting, nor is it the last one. If I would want to, I could do 20 years time skip and use Chiel's and Garrett's son (the MC) as the next protagonist, his name is Cade if anyone is interested, I have a story or two for that as well. Or the Naealea's triplets got one for them as well. I have 37 species made with somewhat detailed background information, the level of detail depends on what I used them for.
But that being said, I understand the reservations and do appreciate the counterarguments. But is the story good, bad, better, or worse can only be decided after it is done and shown to the public. And all I can do is weave the story and hope people will like it.