As you say, Banners failed cos they weren't a good buy from the Merchant perspective. I agree.
But affiliate programs don't have that problem. As someone who managed a multi-million dollar PPC spend as well as a pretty good affiliate program, I can tell you that the affiliate program had the best ROI by a country mile.
But onto your point regarding the value of affiliate programs for the publisher - a very valid issue to raise.
I understand what you are saying, but I think you are really underestimating the earning potential of affiliate programs from a publishing perspective. I make a lot more from affiliate earnings than adsense and it's growing as I become more experienced as a publisher. Most of my new sites don't even have adsense or anything other than affiliate links. There are plenty of professional affiliates making a lot of cash from afifliate programs alone. A lot of them regard contextuals like Adsense as "page leak" and refuse to use it. From my own experience as a publisher, I have to agree with them.
For a webmaster who knows how to get targetted traffic, affiliate programs are usually a better option. For a webmaster who only knows how to get general traffic, then adsense and contextual options may be better.
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