See Add multiple plugin directories for one way to do this.
In an earlier project I did something similar, but I used a dedicated theme options page for my theme plugins.
Looking back … I wouldn’t do that again. Plugin updates are a too complicated, separated version control setups too. The client wasn’t always sure where to look at when we were talking about plugins.
And sooner or later you may want to re-use a plugin from theme 1 for theme 2 – you end up copying files back and forth … far from ideal.
You can bundle multiple (single file) plugins in one directory inside the regular plugin directory. In your theme you can use is_plugin_active() to check your requirements.
TL;DR: Keep plugins and theme separate. You don’t save any work by mixing both.