I binged the first season about a week ago, and am up to date on the current (2nd) season - 8p CST later tonight can't get here fast enough!
I am of two minds on the 'show should stick solely to the virus plot' vs 'expanding the story, ie Primaries' debate. Trying to stop the Army of the 12 Monkeys from using the virus that wipes out most of humanity should remain the core plot point, on that I would agree completely... but there does need to be more story to tell, because if it takes X-amount of seasons to reach an end point against just one thing, it would just get quite tedious to watch after an already aired number of seasons.
I don't think it was just "let's try something different" by showing alternate realities and having characters continually bringing up that 'Mother Nature' and 'Time' are entities that are not meant to be messed with. I find it realistic and believable that there are consequences to time travel and changing events, even if done with the intention of trying to prevent horrible things from happening.
I, for one, am hoping Cassie & Cole can get back on that stong friendly (& a little bit more) wavelength they had going for most of S1. I don't expect anything more than that right away - maybe not even at all this season - but hopefully this new fractious paradigm will not last much longer. That, and the idea of her & Deacon, (possibly) together, is just not good for mental harmony.