Also, I think you should choose equipment which best suits the experiment, not other people.
While I think that's true, a paper can potentially be much more impactful if its' results can be easily understood by others, and isn't that really the point of science? In that sense, it's better for the author to stay away from niche methods and tools unless absolutely necessary.
However, I believe that moving to R is not the answer, as you will still be riddled with a lot of the problems that you faced in Stata such as a quirky syntax (except backticks. I hate those backticks). Maybe Python will catch up (I doubt it, what we need is a DSL, not something too general that requires loong commands to do a simple regress). My best bet would be Julia, but it's still a long way to go regarding things like missing values.