R makes it hard for teams to collaboratively develop code in libraries. No, R packages are not a solution, because each user has to "build" and "install" them every time another user checks in an update.
R doesn't have a debugger on par with Python's pdb. It also doesn't show you tracebacks by default when errors occur, which is a huge problem for mere mortals when something goes wrong.
If you're working alone, using well-tested libraries, none of the above will stop you. But if you work on a team, these are big problems (for which Python has solutions built in).
Since you mentioned connecting to databases, let's talk about using MySQL in R. I downloaded a popular package to do that, and found that the function to query the database is called "fetch()". Just "fetch()", not "mysql.fetch()", not "database_fetch()", not "connection$fetch()", but "fetch()". That kind of sloppy naming is par for the course in R, and it's a problem when your project becomes larger than yourself.