The command line is not superficially superior if all you are doing all day is interactively exploring data using R. In that case, R-Studio puts a layer of convenience around the workflow. But, like all reasons that the command line refuses to die across multiple applications (not just R), and is indeed in rude health, wrappers have their downside. They lock you in. They're higher level (lower flexibility). Being a non-essential surrogate technology, they're more prone to abandonment by the developers, which entails more risk to users. They're not doable easily remotely.

Most importantly, if your workflow becomes IDE based, especially on graphics, then you will have a dearth of skills for implementing actual production code that does not rely on a local workstation running a local copy of the IDE in graphical environment. You'll be short of the understanding of how the plumbing works, limiting you to the exploration role of a single-user guy, and you'll limit the shareability of your work.

Sure, R-Studio is great. But no, it's not an absolute good. It's a tradeoff. Know what you're giving up. Personally, I like to use the most generic, widespread version of tools as possible. I can SSH into any computer anywhere and be running R within minutes, with full familiarity with the environment.

By the way, clearly I'm in the minority, and that's the problem. R itself is open source, but R-studio is not. Microsoft has clearly taken a view that they can buy a large part of the R ecosystem, by buying this tool. I consider this to be a bit of a hijack, and that is the last reason why I dislike R Studio -> it is a vector for undermining open source software and in this case, R itself as open to all. All of a sudden, a large (possibly majority) slice of the user base is beholden to a for-profit company and all its incentives. Not me.