found it all pretty simple honestly...
So far we've had storylines stretching at most, 13 episodes or so... while that might be long or complicated for a modern audience, i've had no problems following it or understanding any of the storylines...
people complaining about Doctor Who story arcs being too long... pft... remember the 70's and 80's episodes? One story was between 4 to 6 episodes long... and an arc... Well, The Key to Time arc covered:
The Ribos Operation - 4 Episodes for one story
The Pirate Planet - 4 Episodes for one story
The Stones of Blood - 4 Episodes for one story
The Androids of Tara - 4 Episodes for one story
The Power of Kroll - 4 Episodes for one story
The Armageddon Factor - 6 Episodes for one story
And that was just one story arc... 26 episodes, so 2 new seasons worth of episodes, all continuing on from each other in one storyline... that was enjoyable and well written Who