@Ryan

The problem with that approach, is that you often need to modify the theme to accomodate the plugin in a suitable manner. Many plugins add styling information to the site, and you really need that to be styled by the theme, not via the plugin, or else the plugin itself will require some sort of theming system which is likely to be a pain in the neck.

Yeah, I have ran into this problem of trying to over-ride with some bbPress plugins. I wish that these plugins were left a little more open to the theme's styles. I am going to try to support as many popular plugins as I can with my theme's style, but I suppose you have to cut your losses somewhere.

It is fine line, I agree that AJAX features would be a good candidate for inclusion in the theme. For functionality that actually adds content, like signatures, I could see some users being upset if they switched themes and "lost" that content. I guess they could keep the sigs by tweaking the new theme, but using a plugin seems more self-contained.

We could release a plugin which is provided as a complementary extension for the theme.

That would be cool, even just sharing the extra functionality that you add to the theme as a plugin suite for people that would like to use it on other themes would be well received I am sure!