We are rebranding a large site, about 20K pages. The site structure and code is going to change very little, there will just be a banner change and possibly some small css changes.
We are going to use a 301 redirect across the whole site, and understand there is likely to be a drop in rankings.
What we are worried about is redirecting such a large number of pages ot a new domain. Will the new domain be penalised becuase it suddenly has 20K pages? Should we redirect things more slowly i.e. a section at a time?
There's no reason to worry about a true penalty since your content is all legitimate. Numbers alone do not mean spam to Google. Also, if many of those urls are redirected page by page from your older domain, then you've sent a nice clear signal, much better than sending all the old urls to the new home page.
That still doesn't remove the so-called sandbox period of getting a "trust check-up" for your new domain. But there should be no worries about getting a true penalty. There are many reasons for lower ranking that are not really penalties, and a new domain is one of them.