You'd be surprised about the extent of this problem. I get e-mails all the time from people who are worried that they have a monthly payment for my app, for example. There are just an awful lot of people who don't "get" software at all and derive real value from simplified one-party billing.
So if you start from the premise that billing for iOS apps has to be brain-dead simple, we arrive at the present rule: any payment that looks like it happens on an iPhone must [2] run through IAP at whatever rate Apple can break even. If your payment collection process consists of people using their fingers on the screen of an iPhone, then it is potentially confusable with IAP by Grandpa and he might get mad at Apple; this is unacceptable. But monetizing your pizza ordering app by handing money to a pizza delivery guy who shows up at your house is not confusable, so it's A-OK.
Now, it's perfectly debatable whether or not consumer confusion is really that big of a problem, or a problem big enough to justify the negative externalities of solving it. But if it is, then the result follows: the solution is to run all the billing through a break-even single party. If you accept the premise, then the rule that is fairest and best and also solves the problem is the rule that we already have.
It's unfortunate that we live in a world where the economics of Dropbox, Skydrive, Amazon et al seemingly don't allow enough profit margin to pay Apple's overhead to process payments. But I'm not really sure who is to blame for that: the consumers, for being confused about billing; Apple, for trying to fix it for them; Skydrive etc. for not creating a two-tiered pricing structure to charge IAP customers at 30% more; or consumers again for being unwilling to pay an extra 30% for single-party billing.
[1] http://www.macobserver.com/tmo/article/apple_app_store_runs_... [2] there are some exceptions, I'm speaking broadly to make a point