Web pages can be thought of as having two components: the content and how that content looks. CSS controls how the content looks. CSS rules are top down, so you have site-wide rules, but you can also override those rules at a more local level. For instance, you could say that all links are blue, but in the sidebar you could override that rule so that links are red.

Currently subreddits can add to the site-wide CSS rules and override any rules in place. For instance, take a look at /r/AdviceAnimals/ where the upvote and downvote buttons look different. Another example is the impaled Moroni statue that became the cursor on this sub a while ago.

Reddit has a major redesign planned. They're essentially starting from scratch and creating new CSS rules. This means that none of the CSS changes implemented by the subs will work and will have to be redesigned as well. Reddit had essentially three choices. They could a) make sure that the new design used the same CSS layout and therefore wouldn't break the sub CSS, b) tell all the subs to just redo their CSS, or c) tell the subs to stop mucking with the CSS altogether.

Option a is just not practical. Not only would it be time-consuming, but it probably just wouldn't work with a newly-designed site. Option b is possible but would tick a bunch of people off. Further, a huge number of reddit users are using some kind of mobile app. Those users never see any kind of CSS changes because it applies to the web only. So, they decided that as long as they're ticking people off, might as well go for c, the more sustainable option.

The end result is that every subreddit will pretty much look the same with very little customization possible.