I think a case can be made for both. For many new users, adding more and more plugins can get a little overwhelming and managing them can be as well. If a user finds a theme with all the functionality they're looking for built-in, I think that's an easier way for them to get up and running quickly. On the other hand, I can completely agree that having the functionality in the theme and not in the plugin can lead to potential problems as you change themes down the road. I don't think it has to be one or the other, but I think it needs to be clear to the enduser the pros and cons of their options.