The Comma Rebellion

The rules clearly state to use commas to offset and separate certain words, phrases and clauses.
https://owl.english.purdue.edu/owl/resource/607/02/

CMOS supports the use of the serial comma.
http://en.m.wikipedia.org/wiki/Serial_comma

But when was the last time you saw a serial comma in a fiction novel?

Would you even notice the absence of a comma following a long introductory prepositional phrase?

No one will admit to it, but many authors and editors are not using or requiring commas according to the rules anymore.

Is it a sort of silent rebellion? The writer is assuming the reader is smart enough to figure out the meaning without all those distracting obligatory commas. As much as it pains me, I see the logic. I like to read quickly. Commas don't really make the meaning more clear, most of the time. I rarely slow down just because someone put a comma there and told me I had to pause.

I add very few commas when I proofread. It's painful for me, because it's my job and those are the rules. But who am I to pepper the manuscript with commas that are apparently being considered optional by people much smarter and more experienced than me?

For a content edit, I think it's worthy of a discussion with the author and something that should be worked out in the sample edit.

Many comma rules are already subjective, should more of them be too?
Are the rules just guidelines when it comes to commas?
Do you want your editor to put in commas because it's grammatically correct?
Or do you want your prose to flow without all those restricting pauses, rules be damned?