I have both - AMEX Platinum since 2003 and Prestige since April of this year, so my joint experience isn't long. However, I actually find the two complement each other pretty well. 1) AMEX makes me choose an airline for reimbursement while Citi doesn't; 2) Since they each have GE refund, I applied for me and my wife; and 3) Citi's hotels aren't necessarily included in AMEX's FHR program so I have two sets of hotels to choose from.
However, to answer your question, if push comes to shove, I would choose AMEX - with any purchase or travel reservation (I've only used the Citi card when it resulted in savings, not for everyday bookings), I trust AMEX wholeheartedly, and I feel more comfortable using them.
Also, out of curiosity, you mentioned that using the Citi card to book WE hotels doesn't result in earning points? Does this mean if I book a WE rate at a Hyatt, I won't receive Gold Passport points?