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You probably won't notice much. Things work just as they did before. If you notice anything, it'll just be that everything is super consistent now (there were some inconsistencies in how the syntax highlighting looked before). It's a good change for us, because everything is one consistent system which is easier to manage. Good for you, because it's going to be a lot easier now for us to offer more options (more themes, more fonts, etc).
One thing we'd like to offer (as soon as we can, no promises) is choice of syntax highlighting for Embedded Pens. It's tempting to do it the same way as everywhere else, where the logged in user's preference is what is used. But we're thinking for embeds it's probably important for people to force themes that they prefer as an aesthetic match for their site. Thoughts?