This plugin makes some fundamental changes to WordPress core functionality.
The plugin author does not adequately warn users that using this plugin can cause major issues. We’ve done tech support on literally tens of thousands of WordPress sites, and have seen this plugin break things many times.
A plugin like this is really ill-conceived in the first place, as it makes major changes to the functionality of other plugins, with having a keen understanding of what they do.
We’ve done compatibility testing and tried a while back to create a compatibility solution.
Additionally, instead of working with other plugin authors, the dev, Jeff, decides to go adversarial, instead of taking a collaborative approach. In the latest update 9.2.3, he added malicious code that specifically targets only WP-SpamShield deactivates the plugin, and uses technique that prevents site owners from reactivating it, even when Plugin Organizer is disabled. (Full disclosure, I’m the lead dev of WP-SpamShield.) That’s not acceptable, as this is a leading anti-spam plugin, with almost 200,000 users. Plugin Organizer is leaving potentially thousands of site owners without anti-spam and security protection provided by WP-SpamShield, and without them knowing that this is happening. That fits the definition of malware.
It would be easy to provide a hook or whitelist feature that allows other plugins to opt out or opt in. That’s essential because not every plugin should be interfered with.