This is just my gut speaking. 
But I think that even though themes and plug-ins are technically the same, they are pretty different from a user’s perspective. Especially if they have experience with other blogging platforms.
So if it were up to me, I would hide the implementation details from the user and just let themes be themes and plug-ins be plug-ins. Keeping everything that has to do with themes bundled together, like browsing available themes, installing, and making overrides. And the same for plug-ins.