Indeed - I think it's unclear how you should begin to teach R now. There is a lot of legacy stuff that you may need to recognise if you want to understand the help documentation. But if you wanted to seriously work in R it maybe better to skip straight to ggplot2, dplyr and broom without touching base R, the apply functions, and list in list in list hell.
That's pretty much what I did. I dip back down into the 'base' stuff when I need to, but in general I stick in the hadleyverse of tools. It's been great.