I haven't moved to iAds yet, but from my experience the CTR is at least partially dependent on what ads are being shown. Some ad networks will get consistently better CTRs over a given period of time.
I've already mentioned that I usually get double the CTR for my own custom ads. Those ads are obviously highly targeted to people who are already using my apps.
People aren't likely to click on the same Nissan ad more than once. So if that's all that's being served, you're not likely to get more than one click per customer. That's one click per customer, once, no matter how many apps he owns that show iAds.
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