I want to start by saying, the people who got downvoted, should read questions carefully before they answer. Because the question didn’t ask for specs. It asked about the difficulties while choosing a Linux distribution.
This is a bit hard to answer.
But I’d say, the first one clearly is, that you don’t know how the distro is really going to behave in the long run and when installed, especially when it comes to upgrades. The upgrade process is one of the most problematic of all. Not only for various Linux distributions, but for various operating systems in general. Windows for example too has tons of problems with the upgrading process.
The reason for this particular problem while choosing a distro is, that a live system is a snapshot in time and you don’t upgrade live systems. In fact, running a live system from USB, even the whole performance is completely different, since the drive the live system runs on and the ports are way slower than an internal hard drive (both, HDD and SSD!).
Second one, I think, would be to grasp the actual proportions of the distro of choice. This is mainly about purpose and the dedicated repos. It’s not impossible. But before you install the distro, it’s quite hard to find the according repos and gain an actual oversight of the provided tools. In fact, you would have to research all the tools you are going to need beforehand. That’s pretty much impossible. So, it’s hard to know, how close the distro really is to your purpose.
Hmm… this is really hard. You can find out a lot by just testing the live systems. Of course that would be another problem. Distros that don’t provider live systems. Distros like Arch Linux. They are rare though.
What could be the third?… Maybe that one! Since you don’t know the problems you are going to run into in the long run, you also don’t know the quality of the support, community and Wiki while choosing the distro. This usually too reveals over time and when you run into the according problems and errors.
Maybe that’s not the end of it. But that would be three problems I can come up with, while choosing a distro.
Stuff like hardware support and GUIs are not problems. Because you can test live systems and GUIs against each other to find out about the basic hardware support and choose the GUI that fits your taste. But choosing a distro is a short-term process that doesn’t show you long-term problems. That’s where the difficulties are.
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