Dropping the site design change from the graduation package is understandable. It is obviously a large amount of effort to draft, consult, and implement a design. I agree that lack of a site design is a poor excuse for holding back the growth of a site. I've lobbied hard for this proposal for a long time…
… with one difference: the privilege levels need to be raised too. If privilege levels aren't being raised, then it's not a true graduation. The site design is cosmetic and thus optional; the reputation thresholds are neither cosmetic nor optional. Using thresholds that are supposed to be appropriate for a new sites on a mature site is harmful. Dropping the threshold change from the graduation package is demeaning.
I assume that with the exception of the site design, all of the changes shouldn't take more than a few hours of work to implement. There is therefore no reason not to give graduated sites everything but the site design.
If you want to give users something to celebrate, I suggest that you apply a generic graduated site theme that is different from the beta theme. If the design team is too busy to do even that, though, then let's drop even that request — Code Review wants this done yesterday!