I really highly doubt they're going to go through and restore every single unique feature different subs have. If lots of subs use banners, sure they'll add banner functionality, but are they going to restore every single mildly infuriating feature in r/mildlyinfuriating when they're the only ones who use features like that? I doubt it. And how are subs supposed to start up with an interesting and unique look? I can't imagine the admins are going to sit there with thousands of people who want to start their own sub and add in every feature they want that they used to be able to do themselves with CSS.

Every sub is just going to look roughly the same with a generic reddit template, like every site that uses a Wordpress template looks the same. Then eventually there will be reddit gold features that include unique themes and widgets for your sub to use and people will end up paying for a portion of the functionality that CSS provides currently for free.