We're seriously considering converting our Santana Nuovo handlebars from drops to flatbar. My Captain's back is getting stiffer and it's getting less comfortable to manage the bike with the drop bars. We've ridden flatbars and drops on other single and tandem bikes in the past and understand the arguments for more hand positions in the drops, etc.
If you have stems with front plates that can come off, you can easily take of the drop bars and mount a flat bar just to sit on the bike. You might find you really like/hate it?
My only word of experience, having done both. As a short legged captain, I find drop bars for the stoker easier to swing my leg over. Flat bars for the stoker seem to extend forever and I think I'm going to fall over half the time when getting on the bike. I'm sure this is due to my short legs and frame that never seems small enough. I only point this out because there are weird things that happen when you change your tandem, so don't be surprised if something random gets easier/worse with your change.
IMHO - setup your tandem however makes you ride it the most!
simon