The problem is that only a handful of plugins offer the user an option of what to do with data at deletion at all…
And, even with a plugin that is not vulnerable, but that you just want to replace for some operational reason, all that stuff accumulates bloat over time.
Especially in the wp meta table.
It really inflates the size of the installation.
And a lot of experts agree that installation size have a definite impact on the site performance.
I’m not suggesting that there is a one-size fits all solution to this.
There isn’t.
But it does need to be considered and addressed.
A sample plugin can reduce the problem. Or generator which bootstraps a sample plugin - minimalistic set of files and options according to current recommendations, standards and best practice. It may even have a child page in admin panel (Tools section for example) to configure it. Plugin meta data, some code snippets, screenshot, links etc.
I mean that including “uninstall.php” and other best practice in sample plugins is a nice part of a learning process. This method avoids setting strict rules but stimulates building high-quality (close to guidelines) plugins by providing contextual examples and references. I bet this is more effective than just trying to force standards technically or to change developer habits via external handbooks and manuals.