I know that feeling and you're right though, Chase and Leo is the most fit couple as far as ik and i loved it so much. But after the way Clint and Flynn talking so seriously about Leo's true nature (unstable), then since Leo finally known as 'Echo of Life'. For me the most rational reason is to reject him and made him realizing all his mistake. (you know what happened in the train if we didn't reject him)
And MAYBE it's quite possible to get happy ending with Leo IF he doesn't created as "one of the Echos" and doesn't have an unstable personality like he does in the game (idk that's ma opinion)
About what's really happening in Echo Town, maybe we need to pass all route such as carl, jenna, etc. And to knowing more about Sydney