Many changes have happened from season 1 to season 2: the title card and theme song are changed to remove everyone and only feature Ellen's face; Ellen describes owning the store as the outright buyer and owner and only Adam and Joe remain as main characters alongside Ellen. However, the layout of both the bookstore and Ellen's apartment have not yet been modified, in the beginning of season 2, as they are in later seasons.
No respect is given to neither the 2 actresses who were dismissed, nor to the audiences as to what happened to their characters---Holly and Anita. (Anita did not even appear in S1 finale.) Instead, Joely Fisher's annoying and cantankerous character is already firmly in place, also without explanation whatsoever as to who she could possibly be in relation to Ellen, since she was never seen before. Worse is yet to come: the even more annoying Clea Lewis character of Audrey making a return with a newly found perky-to-the-max personality, and the even more cantankerous Jeremy Piven as a cousin character. It is unclear why Ellen decided that adding angry after angry and/or annoying characters marked an improvement for her sitcom. At least, the absence of her boss Suzan is explained by a couple lines whereby Ellen states now owning Buy The Book store.
The first season of the show was called "These Friends of Mine," which changed to "Ellen" at the start of the second season in order to not be confused with Friends (1994).