The alternative is to not use a publisher and sell the game directly.
This isn't a novel concept; it's been done forever. "Shareware" distribution and subsequent direct-sales to interested consumers was a popular early example. More recently, one might have seen games sold directly to customers via a developer's own website.
The services publishers provide aren't really necessary for success (although they certain improve one's odds). In the past, publishers were basically one's only real option to get console platform access and retail distribution channels. But the difficulty (and importance) of those perks has waned somewhat. It's arguably more possible than ever to successful self-publish a game, or in other words, to be independent.
Today there are also useful compromises available, as well; options that provide some of what a publishing deal might as well as only some of the long-run cost.
For example, distribution via Steam is far more open than distribution to yesteryear's major retail outlets ever was. Valve provides basically no other services on top of what everybody gets on Steam by default, but what they ask from you in return is similarly much less.
And companies like Kickstarter provide a more direct, grassroots mechanism of raising funding. Kickstarter doesn't ask for recoupment, they simply take a portion of the money you raise.