The first episode of this season was certainly very different from the first episodes of the first season. Kinda feels like Seth always really just wanted to make a Star Trek (like) show and only put in humour because that's what Fox (and maybe fans from some of his other work?) wanted. But the Star Trek / Sci Fi crowd pretty much loved the "meat" of the story and the setting and with every season he dares (or is allowed to) go deeper into it. It's not Galaxy Quest [serial numbers filed off]: The TV series anymore!
I might miss some of the humour, but there was also a lot of stuff that just took me out of the story, particularly in the first season.
Unfortunately, I didn't remember enough of the details of the last season to notice that Charley falsely described Isaac's actions, but it felt a bit off to me at least.
I think "racist" Wesley Crusher doesn't really fit as characteriziation, though. First, racism already feels a bit too much like a departure of the whole Wesley Crusher deal, but Wesley was also a kid, and also the kind of character a kid might identify with, possibly also an author-insert - Charley is a trained officer with some experience and some unique sci-fi talent and just doesn't fit.
She's just a talented character, but she has a bad attitude.
In terms of Sci-Fi Captain comparisons: Ed Mercer would have ordered Worf to donate blood to the Romulan.