In case anyone's curious, the short answer is:
Plugins within plugins are problematic. A plugin embedded in another won't be loaded as a plugin and won't function as intended. (Unless, of course, you open and save it after installing the parent plugin, "upgrading" the child plugin from shadow tiddler to a full-fledged tiddler.)
Also of note:
Tiddlers from the core are loaded before any user-created tiddlers (including those loaded from plugins), so you could indeed create a personal core of settings and core tiddler modifications or replacements that would override the default behaviors of a vanilla TiddlyWiki — as long as none of the tiddlers within that personal core were plugins themselves.
The $:/core itself has a plugin-priority field with a value set to 0. At a glance, it looks like plugins with this value set are evaluated first, in ascending order of value, then plugins without a plugin-priority are evaluated. So if you wanted to create a personal core to overwrite the TW core's functions without impacting any other plugins you might install, you should be able to do that by giving it a plugin-priority of 1.
A better solution than a personal core may be a personal plugin library — akin to what Jed and Tobias have created for their plugins. In my case, I'd put the library online, and anyone who wanted to pull from it would be welcome to, but the real intent would be to make my customizations, settings and plugins available to me. I'd create a small plugin pointing to my online plugin library; drag that into a new, empty TiddlyWiki; and then use it to import my collection of personal plugins (and other assorted, sundry tiddlers) from my online "TiddlyWarehouse."
—
Jeremy devoted some time to this notion (and the bigger, related notions of bundles and TWederation) in Hangout #98.
You can catch the relevant bits here:
... starting at 1:35:17 and continuing to 1:52:05.