The biggest problem with Linux is the people who have problems with Linux
Face it. Linux is not a commercial product. It was never meant to amass vast amount of money from clueless people as its sole purpose. Linux doesn't have to cater to the mass. There is no reason to.
It was created to scratch the itch that people had in the computing world. And they formed communities who had similar itches so they can scratch common itches together.
The biggest problem is the people who have problems with Linux. If they have an itch, don't complain about Linux. Form a community to solve the problem. Pay someone to solve the problem.
Linux is not a free handout for lazy people who expect hand holding in every step just like in commercial products. The "free" in Linux is "freedom", not "gratis". Freedom to tinker with it to solve problems. Then share the solution with others, so others can improve it and give the improvement back.
It has to come from the people. If people want freedom in software, work for it, but don't treat it as an entitlement.
The next biggest problems would be software patents and shady monopolistic practices that hinder innovation. But again, these are controlled by those who would like to amass revenues from lazy clueless people who don't care about true freedom.
So back to the biggest problem: The people who have problems with Linux and expect free solutions without contributing anything.