Regarding integrating plugins into the main branch, there's upsides and downsides.
* Plugins can be updated independently of the main executable, and can be developed independently and with different coding styles the author is more comfortable with.
* Plugins can use external dependencies or string resources, which may bloat the overall size of the executable. Most plugins are niche use, and majority of the users never use them.
* More features added to PKHeX is more for me to maintain and clean. Not all implementations are reusable/extendable... If users ask about functionality of an editor that I didn't make or report a bug, it might not reach the original author for triage.
* Most plugins don't document their code thoroughly, making maintenance / other-reader comprehension more difficult.
* Plugins can act as a self-contained environment to play around & have others test, without needing the full executable.
* Not everything has to be a plugin or integrated with the main program; they can be standalone editors as well that reuse the core-project for exposing the save file operations and game strings.
* Different licensing being possible for plugins. Some people don't like GPLv3, or MIT.
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* Dynamax Adventures plugin: makes flipping the dynamax adventure flags easier. Stock PKHeX can still toggle flags via the Block Editor, and you can automatically import a list of block names via the "SCBlocks.txt" feature. Most users don't need to reset event flags, when genning exists.
* Clothing: allows individual clothing piece toggles; tons of names. Stock PKHeX can import and export the final block; most users don't need to customize individual flags.
* Feebas: Most users don't need to calculate position, when genning exists.
* Auto Legality: Relatively big project with its own dependencies; separate development that ties into Stock PKHeX.
* Raid Plugin: Relatively big project with its own feature set. Separate development that ties into Stock PKHeX.
PKHeX is a hobby project; there's always more PKHeX can do, but there's only a finite amount of development attention. There is no auto-updater; infrastructure for that would take time + money (bandwidth). Not really worth when PKHeX isn't monetized.
There are plans for migrating away from WinForms to MAUI later this year; yielding native mobile/non-windows platform support. Less editors for me to port = less work for me to be stressed about. There are many other large(r) projects (like Notepad++) which have their own plugin system.