I understand your concern, but I am of the belief that a lot of Season 2's issues came from arc problems which probably happened due to Berg/Harberts being fired midway through. My own personal guess is they felt like they had to pulp their plan for the arc because they didn't want to have to pay them for the remainder of the season, which led to everything being awkwardly bent to fit into the new "Control" idea.
Of course, they also oversaw the awful season one. Maybe the second half of season two was rewritten because someone decided it was bad. I don’t assume what we got was worse than their original plan.
The second half of season two was weak, but I suspect the things that made it weak — the absurd stakes, the OTT CGI, the witless wrapup in the finale — are now just part of the formula for this iteration of Trek. So I’m less inclined to the charitable view that production problems are chiefly to blame, and less optimistic the show will suddenly find its feet in season three.