Luckily, I think most of the cons can be addressed, except for those dealing with the business model.
Leadership does not try to retain lower staff; they just assume they will leave for grad school (when really they could develop younger staff). This feels like a missed opportunity for an organization trying to be an alternative to PhD programs.
Projects often have very limited funding and are themselves limited. You don't often get to work on what you want to work on or what aligns with your interests. You are pretty subject to the whims of your supervisor/project availability when it comes to your work.
Most of the time the work is small-minded and very limited by funders (whether financially or in general scope). The business model (total time accounting; you cannot charge most codes for work not done explicitly on that code) emphasizes doing the research at the lowest cost, which contributes to this mindset/tendency.
Leadership claims to be devoted to certain values (valuing race equity internally and in the work produced, promoting work, etc.), but does not always stand by hard decisions or support staff decisions based on directives given. Leadership seems never to take a firm stand on their decisions, unless the decision is to "hold a focus group" or "get more input from stakeholders."
Higher level researchers prioritize what will get them money over good/impactful research; they assume that the research they do is important because it gets funded. This is not really their fault; this is supported by the business model.
The organization claims to be extremely friendly for family-life balance, but doesn't observe holidays that schools observe (so parents have to work while their kids are off school).