This will be a short list.
I've been a watcher of "Doctor Who" since the fourth doctor, Tom Baker. I fell in love with those episodes. "Genesis of the Daleks", "The Talons of Weng Chiang"...fun stuff.
I've been watching the new shows, and while they sometimes are fun (the "Blink" episode was great), I feel the show has lost its way. It's become silly, too melodramatic (i.e., the relationships between the doctor and his/her companions always devolve into weird, over-the-top sentimental expressions; those who have seen the show of today know that of which I speak).
So, with that in mind, here are some suggestions. If you disagree, I don't mind, please let me know. I am interested in other viewpoints.
1. Make episodes concept-based, not character-based
Don't get me wrong...you need strong characters. But let the episodes communicate characterizations seamlessly within the plots...don't have gut-wrenching stop scenes where the show has to present five minutes of a companion, say, talking about an irrelevant character-building exercise...just do that within the show itself. And start with the concept. Think of "Blink" and the Weeping Angels. The writers should say something like, "What if we made an actual bottle episode (as in the Hollywood-economic definition of the term) inside a bottle? The Doctor is trapped within a bottle and has to get out." Come up with something you hope to be clever and then write the episode around it. (Has the show ever done a bottle episode like that? Perhaps it has, but I don't know.) Or how about this: the Doctor has an episode where he/she goes into the videotaped world of the older seasons, and interacts with those adventures? Or, maybe the show just lenses an episode in that style with no explanation; it would be fun!