I can see why Braintree would have no interest in businesses that are destined to maintain smallness, but they're missing out on getting into bed with some young companies whose payment volume will eventually pop. And leaving the door open for a more nurturing payment portal to grab young companies (and presumably keep them).
So it might be wise to for Braintree to loosen up the fees a bit for promising young companies - an incubator program for payments of sorts. At least for the YC/HN community :)
Though, honestly, looking at their pricing, Braintree ins't crazy expensive even for a company that gets $0 sales out of the gate... $99 initial setup, $35 monthly, $10 for cc storage, $75 as a zero sales "penalty". Setup delay seems to be an issue here as well, but that just seems like Braintree doing its diligence.