Just had that conversation... Everybody charges per repo and that's pointless. Charge for disk space and let us have unlimited repos. I would sign up for monthly plan then.
Github wants to price discriminate between serious users who can afford to pay more, and casual users. Projects with a high development budget (e.g. complex software projects) don't necessarily use more disk space than someone's personal website, so disk space isn't a good way of price discriminating.
On the other hand, organizations with a high dev tool budget are probably more likely, on average, to have more private repos. So it's in Github's best interest to charge by repo count, until they figure out a better way of discriminating between customers.
I for one would buy a micro plan if its only limit was 1 collaborator, but for now I will stick to bitbucket (kiln is free for 1 collaborator in case anyone didn't know through the student and startup edition).
I'd like github to differentiate between private and public repos more, to make the private repo feel more secure. Now I have to look twice to make sure the repo is private. I would also like to have a way to say - this repo can NEVER be made public, and neither can forks.