1. Most Importantly, And This Covers All The Other Items, Do The HARD Work
Take the audience somewhere new--no reset buttons, no history rewrites, no "the companion saves the Doctor... again," no magical, last-minute fixes. Keep the show unexpected, keep it exciting, keep it a source of wonder and imagination. Sure, draw on the past, but adapt it anew. It's one thing for a show to have some general tropes--it's certainly true of any given writer's style, even entire genres, but there's using them and there's overusing them. For example, take this last season. Count how many times something happened that effectively erased, in one swell foop , changes through time. The two most obvious are in "Journey to the Center of the TARDIS," in which the history-changing button literally has the words, "Friendly little button" written on it, and in "Name of the Doctor," where Clara erases everything the Great Intelligence did and then, with the Doctor's help, escapes as if nothing ever happened (Why did River think that was so dangerous? There weren't any complications at all!). In a show which in many ways is about the use of intelligence and creativity to with the day over force, intelligence and creativity must go into the plots. Laziness cannot be excused. Think outside of the box... even if it is bigger on the inside. The world is watching.