Research scientist in industry but I'll talk about something that I lead outside of my job, a project in computer vision designed to basically create a good open source alternative to a bunch of bio-imaging tools behind paywalls. I maintain the code base but work with my old lab to keep expanding and developing (at this point, I mostly do software work/troubleshoot methods from old papers that have weird issues). Currently focusing on anthropology but long term I want to push into computational neuroscience because I have a bunch of problems with that field from both the perspective as and adjacent researcher, and as family of a neurology patient...

Biggest problem is by far lack of existing tools outside of MATLAB, mostly for visualization and signal processing. Python is okay but not quite there in my experience. MATLAB alternatives are more or less in the same boat. The main challenge is that "performance evaluation" is inevitably qualitative. The benchmarks used to publish results aren't quite meaningless but they're mostly for show/make ML people happy. Practitioners don't really seem to care. That leads to a situation where I need really good 3D visualization tools that are interactive. Python hasn't been good for that. Current "free" solution is to go into Javascript but other issues arise because things just aren't configured properly for the space I work in.

The other big challenge is a really high bar for data quality prior to subsequent analysis. Most of my actual work here is spent in filling in niches of computer vision where almost nothing in top conferences/journals applies. This creates another challenge, since I have to do things from scratch. Say I'm registering 3D objects, because that's a lot of what I care about. Textures look mostly okay but have a problem using state of the art method? Rejection because prior work indicates that major findings in the past have been heavily biased by tiny issues...very little margin for error.

Then there's compute. To get meaningful attention, I have to assuming the users will have mediocre compute resources, most certainly no GPUs. Also a big limitation. Can't pre-train much of anything either.

If I had a genie, I'd mostly wish for interactivity in Python to be better because that would take care of a lot of headache...or for Julia or something to be more mature. Lots of interesting research to do and can be done in a short order, bottlenecked by lack of existing tools for intuitive interface design + lack of time to do them, even if I ended up getting paid.