Thaumaturge - should I be using a Staff or Scepter/Shield?

which is better, or preferable? does one do less/more damage than the other?

or is it all personal preference?

Pre- 50 use whatever combo gives you the higher stats. 50... Same deal until you get your, Grand company weapon and WP dark light shield, WP Darklight staff, primal weapons, or your relic. Your gonna use whichever give the highest Ilvl then or stats. You will eventually be in a staff until you get T5 1 handler and shield. Ifrit is a 1 hander, Garuda is 2 hander, and forgot what Titan is but doesn't matter since you kill him you get your relic staff.

You're going to be using whatever gives you the most weapon damage... which is typically going to be whatever is the highest item level you can wield... which is going to change as you level.

Yeah, you'll be switching back and forth from a two-hander to a one-hander and shield as you level to 50. Weapon damage is always your primary concern and by far the most important stat for you. Then Intelligence comes and after that all the rest.