As something of a modern-day heretic, I actually have no problem with flat, C-style PHP code that uses a common prefix for each function to avoid collisions with other code, for simple and small projects.
I find that small pieces of code written in this way are much easier to fit inside one’s head. And since plugins should be kept simple, fulfilling a single purpose… this often works out pretty well.
In fact if we are going to promote specific development practices then my first choice would be just that: keep your plugin code as small as possible. Our community already tends to think this way, and I would like for the ClassicPress plugin directory to include some metrics around line counts and/or sizes for this very reason: to continue to nudge people towards creating and using smaller, simpler plugins.
As far as architectural practices, I suggest learning to write automated tests. With good automated tests in place, the architecture of the code matters less, because you have more flexibility to improve and reorganize things as needed and be pretty sure you won’t be breaking anything. Writing code in a way that allows automated testing of one small piece at a time also tends to encourage better architecture all by itself. This might take the form of classes that don’t mutate global state or composable functions that have as few side effects as possible, either way, the result is cleaner.
It’s also important to keep in mind that plugin code doesn’t operate in a vacuum. It has to interface with ClassicPress itself and that code is a mess with a lot of history and mistakes behind it, many of which can’t really be fixed at this point because they would break the ecosystem that depends on the current behavior. The “best practices” for writing a CP plugin therefore probably shouldn’t be the same “best practices” as starting a new, modern PHP project from scratch.
There are at least as many opinions about best practices as there are developers. We can nudge things in a certain direction but I don’t think dictating specific architectural choices is the right path.