So we will be now selling simple themes with bunch of plugins? I guess it might not be a problem for themes from "blog" category, but what about this very niche themes, like for hotels with booking systems, restaurant themes, directory themes etc. I'm pretty sure it will cause more problems than you're expecting. Imagine you have "directory" theme with full maps support etc, all functionality has to be provided by a plugins, someone buys it, changes the theme, and it works but doesn't look good for obvious reasons. Who's now to blame? Author of a original theme/plugin hybrid or author of new theme? It looks for me like we will be changing to ThemeCanyon.
Not at all.
As an example, there is a real estate plugin in the WordPress.org directory: Some themes will be made to support this and it will work nicely, others will not. This is actually fairly common.
In your example, you could create a plugin that provides all the restaurant functionality for your restaurant theme. If you make a second restaurant theme, you'll likely use the same plugin. If another theme is used with the plugin, it probably won't work, as that theme wasn't created to work with that plugin.
BTW, what about OptionTree that has “theme mode”, does it have to be included via the TGM Plugin Activation class?
See my reply to Jaynesh above.