In addition, peer-review at well-run open access journals, which are the model I think we should be moving towards, does not take anywhere near 12 months, and in CS there are no publication fees (I gather this differs in biology). I typically get very well-thought-out reviews which help to improve my papers in about 6-8 weeks, and if accepted, publication is completely free of charge. And, it's becoming increasingly common to circulate preprints ahead of submission, on places such as the arXiv or at conferences or workshops, to get the feedback of a larger proportion of the community before publishing the final version of the paper.
I agree peer review does not settle the correctness of a paper; it's a system for ensuring a high-quality discourse, not to publish only papers which are the last word on a subject. That's what reply papers, replication studies, etc. are for. I am skeptical that attaching a bunch of points and badges to the discourse is going to improve the quality of that discourse, and suspect it will harm it. I'd rather look at how to improve the discourse by improving the journals. But that won't make money for VCs, so I'm not surprised that we're only seeing it from nonprofit organizations like JAIR and PLoS.