I work remote now, but before I switched to my current job, when I still had a commute (and by Bart in bay area too, no less -- a notoriously uncomfortable commute if you're not familiar), the last backpack I used was this "Slim Laptop Backpack". https://www.amazon.com/gp/product/B00RRHNLXC/
Basically, I realized that pretty much the only thing I needed to carry to and from work was my laptop (13" MBP at the time). I had a few other things like earphones, ibuprofen, etc. but they all fit inside small compartments in that slim backpack.
That was my favorite commute backpack by far. On the train, it lets you not take off your backpack, and still not be a bother to others. It satisfies your bonus points for water/snow resistance if it's raining or snowing, because you can just wear it underneath your bigger jacket.