The EQ protection isn't the only use of the pendulums. The EQ protection really applies to an on mark mono. If you're running a 2 pillar/2 pendulum duo as mentioned, I guess it looks like this:
Mark of air
Air pillar = air
air pendulum = air
Fire pillar = fire
Fire pendulum = half/half
This is a small duo, the same thing you would accomplish with air pillars + air pendulums and mark of fire. However if you keep the numbers even, it will have vastly more air quanta. I'm not saying that is bad, since these duo's already work best. Of course that's assuming you already have more air cards. A simple traditional split (7-8 air and 7-8 fire pillars) for a total of around 15, counting the mark, doesn't really flow very nicely. It takes a few more turns to play either element, or you need vastly more pillars. This is, assuming the air/fire cards are absolutely even.
I think this has some relevance to shantu's example also. I don't know what the mark was, but it seems the distribution was really off. With 5 or 6 pendulums and the mark, you can usually play some small side element cards early. The pendulums shouldn't be overestimated. You will mostly have 1,5 or 2 quanta production per turn. If you consider all that, the pendulums can really make a small duo flow. Of course this is a different issue from the EQ problem. Normally duo's are quite vulnerable to the EQ's, since you could lose one whole element. The 4 way split solves that, if you have all those pendulums that is.