Speaking from my own perspective, I see Beta on Stack Exchange very like Beta on Google. It doesn't really change anything, other than requiring lower rep levels for certain activities.
Looking at the official SE discussions on Beta status and Graduation, it looks like graduation itself is no longer some big bang, changed site, yadda yadda to more of a slow process with CSS updates being separate from Moderator voting, Rep level increases etc.
One of the good things about the Beta sites is they are consistent, so they feel very much part of SE. Development of CSS for graduated sites is a much bigger piece of work than you imagine - it takes the design folks a long time.
That said, if you had a specific gripe with a particular element and wished to suggest an improvement/bugfix, please do as @Erica suggested and raise a new meta post with a bug tag, and the CM's will look at it.