I really like all plotting systems in R. First, I used base graphics for a few years—and loved it. You learn your way around par(), commit esoteric argument names to memory (oma, mar, mgp, mfrow, etc). It feels powerful — you're just drawing on a screen; its history traces to the original pen plotters. Second, I learned lattice. You can't help but fall in love with lattice after a year or two with creating panel plots in base graphics. The biggest learning curve with lattice is panel functions, but once you learn to throw a browser() in a panel function for stack variable introspection, you can do anything. Somewhere on a dusty bookshelf is a well-worn lattice book I splurged on while taking an R course at UCD.
I like this article, because I think for production graphics, the author has a point. If you're placing lines, points, and labels on a screen — you can create anything. You can draw polygons and arcs. It's like drawing with raw SVG. But I'd have a hard time thinking of an exploratory data analysis situations I wouldn't reach for ggplot2 first. Since it looks at dataframe column types (integers, factors, numerics), it automatically matches these two the appropriate type of color gradient. Coloring a scatter plot by a potential confounder is one additional argument to aes(), e.g. aes(x, y, color=other_col). More than once during EDA I've done this and seen some horrifying pattern in data that shouldn't be there. That's a powerful tool for one extra function argument — the cost of checking for a confounder with color (or shape) is essentially near zero.
I'd make the case that this is a more costly operation in base graphics, and is thus much less likely to be done. You may already have your plots in a for loop to create panels, then you have a few extra lines for adjusting margins and axes (rather than facet_wrap(~col)). It took a lot of code to set that up — there's already a lot of cruft when you just need to do a quick inspection. Then you need to create a vector of appropriate size of colors, and then map this to data. Sure it's easy-ish, but it takes at least double the time as color=some_col. In EDA visualization, I want every single barrier to checking a confounder to be as small as possible—which is what ggplot2 does.
That said, I really liked this article because I do agree that going from EDA visualization to production is a hassle. Just after reading this, I remade some production ggplots with base graphics and love the simple aesthetic — which to mirror in ggplot takes a lot of hassle.
What I really long for is a lower-level data to visualization mapping (like d3) in R. d3 is a pain to learn, but it's really the only data abstraction (even though it is a low-level abstraction) that is seemingly limitless in what it does and can do. I always hope for a general data-join grammar like d3's to be the norm, built on top of base plotting (analogously: svg elements), and then have abstractions like ggplot for tabular data built on top of that.