Because they need funding. Research projects take a lot of capital. And you'd need a lot of money to set up an independent journal, facilities, labs, staff, etc.

Like the other response to this said, it's a little more complicated than "the status quo is easier" or "intelligent doesn't mean smart." This is a deeply ingrained system that's existed for a long time, and if you don't operate within it, you don't get to work in academia. You won't get to conduct your research to begin with, much less will you get to the point of publishing it without cooperating with these institutions. There are also powerful regulatory bodies like the APA and AMA who control just about everything in their field. You pretty much have to work for a university, and US universities are of course greedy and corrupt in their own right.

It would be like unseating the DNC, ending the electoral college, and expanding the two party system in America, but on a smaller scale. Plenty of Americans know that these things need to happen, but it's not something where you can just wake up one day and make the decision to overthrow the system as long as you just try real hard.