I think there are two challenges here. First, opting out of major publication venues is essentially sacrificing your career (no funding/tenure). Second, researchers simply don't have free time to start up an alternative publication system. I think the funding agencies can do a lot more here though...
Tenure isn't the last step of promotion for faculty. There's still full professorships, salary increases, named professorships, the chance to advance to administration (if so inclined). So, while tenured faculty have more job security, there are still substantial incentives to publish in prestigious journals.
