You're right that the cost isn't the main issue. It shouldn't be disregarded though: with 2 million articles published a year, a $2,000 cost per article means $4 billion a year that could be spent on more research. To put that in context, the NIH's budget for tackling cancer is $4.9 billion a year.

The main issues with the journal system are the effects it has on the speed and quality of scientific communication. Peer review by two people is not robust, and it is very slow; secondly, the full range of scientific media aren't shared.

These are the problems that, I believe, require an overhaul of the reputation system in science. The only way to incentivize scientists to share their comments on papers quickly, and at scale, is to provide rewards for them to do that.

The range of media that scientists will start to share will be shared on platforms designed for that media type. Code will be shared on Github. Videos will be shared on YouTube. Data-sets will be shared on sites like Figshare or other sites dedicated to handling that content format well.