Unfortunately, although the intentions are good, the additional restrictions imposed by GFDL creates a lot of compatibility problems in practice. Nowadays, the use of GFDL is no longer recommended by default. Unless you specifically need the unique features in GFDL, the best practice is to use Creative Commons 4.0, either CC BY or CC BY-SA (if you want stronger copyleft than CC BY-SA, even the use of GPL is better in terms of compatibility).
The most prominent problem is the invariant sections and cover texts. It allows certain sections in a work to be unchangeable, such as the front-cover and back-cover texts, so that the information in the original publication won't be distorted. While it's very reasonable for a standalone book, but it would be a violation of basic expetation of free software if the documentation is to be treated as a subsection of the software itself. Thus, Debian packages software documentation separately, and classifies all docs with invariant sections as "non-free software". Also, the most common practice to publish documents under GFDL is to say "it's published under GFDL [version], with no Invariant Sections, no Front-Cover Texts, and no Back-Cover Texts" to avoid the issue. But if you already do this, you don't really need GFDL.
The second related problem is that the GFDL is an independent license, so it's incompatible with GPL in both directions. A GPDL manual cannot use GPL code, and a GPL program cannot use code from the GFDL manual. GPL code to a GFDL documentation is effectively proprietary, the only way to use them is invoke the rights of fair use, which only allows a very limited portion of code to be used. Another possible workaround is to dual-license all code in a GFDL manual.
Even Eben Moglen, lead lawyer of the FSF, believes it's problematic. He says GFDL to him is like gravity to quantum mechanics.
> [In GPLv3] By expressing LGPL as just an additional permission on top of GPL we simplify our licensing landscape drastically. It's like for physics getting rid of a force, right? We just unified electro-weak, ok? The grand unified field theory still escapes us until the document licences too are just additional permissions on top of GPL. I don't know how we'll ever get there, that's gravity, it's really hard.
And the third problem is a practical one, the requirement of all works, even for those without Invariant Sections and Cover Texts, to include a full copy of the GFDL license. Again, while it's very reasonable for a standalone book, but it would be unsuitable for other types of creative works, such as short reference materials, maps, tour guide, or photos. The classic example is Wikipedia, if a reader ever wants to copy a section of the article or a single photograph, the inclusion of the full text of GFDL is legality required. It's why Wikipedia soon migrated to Creative Commons + GFDL to avoid this problem.