The author clearly doesn't remember what it was actually like to arrive on a Flash site, and play the fun games of 'where has the designer hidden the navigation today?' and 'oh crap, how do I turn the sound off?'.
Design patterns are there to ensure that functionality works in a roughly consistent manner across different sites, so instead of having to spend ages figuring out an inscrutable interface, the user can easily buy a product or find the information they want and get on with their day.
This is not a trend. This is lots of people slowly figuring out how content should be structured for maximum usability in a web context. Layout conventions will develop over time, as new ideas are incorporated and technology changes, but that's a good thing.
As has been pointed out, books have looked roughly the same for the last few hundred years, but design innovation has only increased, as technology and our understanding of the conventions involved has improved.
The visual design area is more susceptible to trends - a few years ago everything was glossy, then with 'Flat UI' everything became dark blue and a sickly shade of green. But that's ok too. Except for the green, that was horrible.
The danger is with 'cargo cult' design. That's where the complaint against generic themes is valid – a style is used because it's popular without thinking about whether it's actually the best fit for the content and what's to be achieved.