The thing is, would firing Ross Atkins even translate to tangible changes? Or is it simply something to appease the masses for optics' sake? Not saying you don't do it, but I'm struggling to think about how much of an impact that will actually have.
Like okay, let's assume Ross Atkins is fired and replaced by James Click. There are 46 people listed in the official Blue Jays Front Office directory who work in baseball operations. These research analysts, data scientists, software engineers, scouts, and systems developers are ultimately the ones who are suggesting processes, draft decisions, roster acquisitions, gameplans, and even day-to-day roster moves. I think the GM has ownership over broad baseball strategy, but I also think they have less influence on day-to-day than we actually think. I really don't think firing Atkins would make the analysts think about optimizing their models more or 'work better'. There are no 'unilateral' decision-makers in modern baseball anymore (unless you're absolute trash orgs like the Rockies or White Sox). Replacing Click with Atkins actually might not do anything unless you re-evaluate your entire baseball ops strategy and decision-making.
I think in terms of major league trades and player acquisitions, the baseball ops department has objectively been pretty good. Someone identified Tesocar and Lourdes and they became good contributors. The process of identifying pitching at the major league level has led to some great success stories that most orgs could hope for (turning Ray into a Cy Young Winner, Steven Matz, Ross Stripling, Kevin Gausman, Chris Bassitt, Jose Berrios, not to speak of the bullpen success last year).
The biggest negative about this organization is the inability to draft/develop well to feed a sustainable winner. It feels like they haven't cracked the code the same way that high-functioning orgs like the Rays, Dodgers, Padres, and Braves have done where the cupboard is always full enough to have "waves of talent", or to make high-impact trades. And maybe that changes soon with the PDP complex showing results, but that's the biggest slight against Shapiro/Atkins IMO. That the scouts, talent evaluators, and analysts they hired haven't been good enough to yield a good farm system. It's the thing that would keep me up at night most knowing that we haven't drafted well at all in recent years, and unless either the processes, or talent evaluation, or synergy between player development/scouting department improves, I don't know how you fix it, because it truly seems deep rooted.