Yeah, I have thoughts... make only widget enabled themes available to users. It's in the backend already. If you wanted certain sidebar items available on *all* blogs, hardcode that into each theme. Yes, you can do that and have widgets too.
For mandatory plugins (Ie, plugins that everyone uses and are turned on for all) dorp 'em in the mu-plugins folder and make sure every theme has the necessary code (if needed).
Example: on my MU site, I have one optional plugin called wp-counter. Every time I whip up a new theme, I add the if_plugin_exists call to the wp-counter plugin on the sidebar.
I suppose eventually there may be a way to sort of have "fixed" sidebar items that you could magically drop in mu-plugins and have show up for everyone's sidebar. Would take a few poits of coffee (maybe some cookies) and a week or two of red-eye coding though. :D