This would be pretty cool, but I dunno how feasible it is. One possibility is that this will open up the door for custom system menus, much like Custom Firmware on PSP. But actual plugins for the official System Menu probably aren't feasible with boot2. You'd need a modified System Menu, which should be possible now with a custom boot2 which will remove the security checks done by boot2 on System Menu. For those of you familiar with the PSP Homebrew "scene", it'd be kinda like a custom IPL - allows you to boot firmware without the checks normally done. This would allow us to modify the System Menu in ways that would normally brick the Wii, and with these customisations, we could add a plugin system. But without this happening, I believe the best that can happen is preloader style hacks, which I believe are done by editing memory addresses or something. However, preloader style hacks should be possible with BootMii, just aren't added because the idea behind BootMii is brick protection, not system menu hacks.
And on a side-note, theme's are already possible on Wii, legally (I think). You can use Icefire's MyMenuify to install them. According to him it's legal, but then he also made Wadder and said it was legal, so dont try it till we get confirmation from someone more knowledgeable