All of the statutes regarding document retention and the handling of classified material were in place during Clinton's time at State and for the most part several decades before that. Some additional guidelines/clarifications were put in place after her time in office but they had no fundamental impact on her violations.
For example, Obama put in force a direct time table as to how long before documents had to be transferred to archives whereas before it was more of a vague "in a timely manner" type wording. On document retention charges Clinton could argue that 2-3 years after leaving office and under threat of subpena was timely (and she has several times in the press) and it's possible she could find some jurors to agree with her, whereas Kerry wouldn't be afforded that excuse because it's now set in stone the exact number of days he has to send all his work documents to be stored. On the more serious charges of handling of classified materials, on the other hand, the same rules apply to Kerry as they did to Clinton.