If you read the PDF spec from the late 90's, it is Stephen King novel-scary... container format, multiple encodings, encryption, embedded binaries, embedded JavaScript and more.
This is especially apparent when trying to edit arbitrary PDF files, which is sometimes not so easy or even impossible. Just the definition of fonts and the text layout is already so complicated that this is the logical consequence.
But perhaps the format has simply grown and led to additional requirements such as PDF/A, PDF/X, PDF/E and now PDF 2.0, the next standard that makes everything even more complex... Will this every stop?
PDF has the semantics of a digital print that is resolution-independent and supports copypaste and search (mostly by mapping glyphs back to text).
In addition to resolution independence being something that's higher-level than strictly "digital print", being able to capture transparency is such a higher-level feature.
From the above perspective, PDF peaked in 1.4 when it got transparency support. Supporting roughly the PDF 1.4 feature set was that allowed the Mac Preview app be good enough for Mac users so that Apple could stop bundling Acrobat Reader with Macs.
After 1.4, PDF has gotten better compression algorithms that don't really change what the format is about. PDF/A and PDF/X fit well the notion of PDF as "digital print".
But Adobe has been trying to leverage Acrobat/PDF to other areas that don't fit the notion of "digital print". These include pre-Macromedia acquisition attempts to make PDFs a more dynamic platform and later inclusion of 3D models in PDFs. Other PDF viewers still work for users most of the time without this stuff, which is a signal of what PDF really is to users ("digital print").
(Filling in paper-like forms, while not true to the notion that PDF is a final-form format sort of make sense from the point of view of digital paper, though.)
While that certainly does play in Adobe's favor, the complexity of the spec. is also what occurs when over time new features, some never even envisioned by the original creators, are bolted on to keep the whole "relevant" and/or to add new "features" to keep the 'thing' from becoming obsolete.
We can certainly argue whether the addition of different features was worth the complexity increase, but simply taking an existing system and bolting on the latest "hotness" to use to add to the checklist of "why one should upgrade" features also produces similar levels of complexity.
So some of the complexity increase is merely the fact that the pdf spec. has been evolved to do things it was likely never designed to do in the first place.
Or PSD, for that matter.
On the other hand, the Office file formats (especially Word) have many un- or underspecified cases.
[0] The only one I know of is finding the end of compressed inline image data.
Regarding Reader, I work with PDFs a lot, and the majority of issues have a fairly common pattern. The supplier has created a PDF in a 3rd party tool, which is invalid in a subtle way (production printers in particular are very specific about what they want to accept).
But it works fine in Adobe Reader, since it was built to be very tolerant in what it accepts, so it's often hard to convince the non-technical users that the file has an issue. It's great for end users but has meant that a lot of tools out there just didn't have to try too hard to make PDFs that mostly work, so programming workflows can be an issue.
The advantage of the office formats is they are Zip files with a ton of XML, ie they are well defined. The application parts are another matter of course.
Like every bit of business software, there’s a load of stuff that shouldn’t be in there. It’s a really flexible container format though, and every one of these features went in because there was a need. Times change, things change and it could do with a tidy up, but it’s probably impossible without breaking everything for a load of businesses.
Although TempleOS clearly is a divine revelation.
Although virtual machine hypervisors don’t automatically update, unlike Adobe or Windows.
I’m seriously close to banning acrobat the program for my employees, just haven’t found a rock solid alternative that I can trust to not implement the same dumb parts of the spec.
Not to mention that it is actually horrifyingly slow compared to most of the viewers that I tried.
PDF "core" is not that bad, but 90s "multimedia" craze turned it into badly designed graphical application runtime.
Still, both formats are too much printing-oriented. Reading documentation in PDF on computer screen is not especially pleasant, and unbearable on phones.
Though obviously not the full thing. Nobody does that. Not even Adobe does that.