I'm afraid a Dalek would be almost unplayable. Even in alien-friendly future settings, a Dalek would always be seen as something to destroy or flee from immediately, or be suspected that it's up to something or trying to kill everyone. It can't be disguised or explained away either. It's worse than the good drow problem of D&D. The sourcebooks themselves are hard against it.
I suspect a friendly Dalek would be mostly restricted to the base or ship of a specific sort of setting, and rolled out only against certain foes.
I say that as someone who thinks Kroton the Cyberman with a soul was an awesome companion:
http://tardis.wikia.com/wiki/K...oul_of_a_Cyberman%29
I'm strongly leaning towards a Time War campaign, starting off by running a modified version of "The Doom of the Daleks" campaign from the
Eighth Doctor Sourcebook. I've already thought up two story arcs to follow, set during the war and the aftermath on Gallifrey (turns out the Doctor didn't save it so good after all...)
The other idea I'm attracted to is a
Farscape/
Guardians of the Galaxy-inspired starship campaign set around the year 2590, where the weird aliens are things like Alpha Centauri and Ice Warriors. Derivative, but it could be fun. But I don't have any specific ideas yet, and need to invent more stuff from whole cloth (I like to use adventure modules and existing settings as starting points to build my own adventures.)