If I was granted one wish in this world it would be to take the helm of Who (and making it that much better, from what I believe could be improved upon).
Here goes:
i) 2 parters -yes & for about 2/3's of the stories, They work that much better in that they allow just one, potentially great cliff hanger & also allow better pacing/ other characters to develop, (where stories could benefit from this). Old Who got into a regime of finishing season's with the longer story (a 6 parter). Avoid this. Keep the punters guessing (including what's coming up via the net).
ii) Keep it simple, stupid. So what was the peak of Who? Many including me would argue almost every story under Hinchcliffe -the 1st 3 seasons of the 4th Doctor, was just that. If you watch these stories, yes, they borrowed heavily from standard horror stories of the past, reshaped them, but kept them simple and straight forward. The best ones of NuWho, particularly the last 3 series have been the simple, light hearted, stories with no story arc.
iii) Get rid of a lot of the OTT musical accompaniment scores. They just get in the way, There's a wealth of examples from old Who where the music really works & it is not too excessive. e.g.: The Aztecs, The Web of Fear, The Silurians (parts of). Backings that could still work today.
iv) Lose the melodrama (please). The Doctor is more and more a human (and a big girls blouse to boot) with every passing season. I think he needs to get out more, not pick up so many young human girls, maybe go back to his own planet & maybe find another Romana I type. Or better still go and find Romana in E Space, maybe Romana 5 (Romana is only on 5 lives as she doesn't need to battle so many nasty characters via less inter-stella space travelling).
v) Introduce some real spooky "human-like" aliens. I actually think you don't have to spend a fortune to make someone look quite creepy, & often the more they are like us the more creepy. e.g. no hair, no eyebrows, slightly different cheek bones or forehead via very minor prosthetics & slightly different eyes via contact lenses.
vi) Bring back the Master (but avoid Simm at all costs).
I believe they are going to bring back The Master, so that's one, with the lose the melodrama, there's a fair chance there will be a lot less of that with Peter Capaldi (fingers crossed).
Follow the above & turn a good show into a great show.