See companion question here.
I realized that after I posted my previous question that asking that question might be a "solution in search of a problem." I'm interested in what people perceive to be their biggest bottlenecks in doing great work in independent research.
I actually reflected on what points were holding me back as independent research quite recently.
A major point seems to be a lack of research oversight. This isn't so much about accountability for getting things done, more to have somebody thinking objectively and providing a detached perspective on which ways to address open-ended problems and when to change directions, etc. This kind of management isn't necessarily well done in academic research (at least in my experience) but I have recently found that Jason Schukraft's management style has been helpful for a project that I'm working on with him at RP.
Another I've noticed is that it can be hard to prioritize my independent research over competing projects that I already have in progress with academic researchers (or getting drawn into new projects with people who I've already published with - although I'm getting better at saying no to new things). In most cases, I think my independent research in physical virology is likely to have much more impact than continuing research in my former field of visual biophysicis, but dropping an in-progress academic project (particularly if I've been paid to do some work on it previously) feels like a strong violation of an academic norm so I tend to stick them out until they are done. These projects usually also involve working with a larger team of people, which is also appealing when you are used to working alone.