My biggest issue with the Alex/Maggie pairing is that Maggie's dialogue makes it pretty obvious that she's not going to see the season out, one way or another. Of course the fact that they out and dropped a of of where Alex was going character-wise in season one didn't help either
The truth is, I've been rather meh on the retooled Supergirl. They've basically dropped the office dramady elements which for me was one of the major selling points and what made it stand apart from the other CW Superhero shows. Yes, it's a little more focused, but at the same time, it's done such at the expense of a lot of its distinctive elements.