My personal biggest hassle with LibGDX(The second biggest reason I wont be using it, at least for now), is that it assumes that I'll be developing to multiple platforms at once.
I don't give a shit about mobile platforms(If I did, I'd learn to code in their native language, e.g. Objective-C for iPhone/iPad(Yes, I know, Android uses Java, but I don't use Android and don't care much for their broken market and fractured platforms)) and I don't care about WebGL either, so I rather dislike that the default setup of LibGDX forces me to have several projects in Eclipse, just to make a simple desktop game.
I managed to set up LWJGL, with javadoc/source code attached, far far faster than I figured out how to setup a LibGDX project.
LibGDX doesn't force you to do anything... It is dead simple to set up a project for desktop only.
1) Download LibGDX (stable or nightly, doesn't matter)
2) Open Eclipse
3) Create a Java Project
4) Add libs: gdx.jar, gdx-natives.jar, gdx-backend-lwjgl.jar, gdx-backend-lwjgl-natives.jar ... attach the sources if you want.