After a quick bit of Googling it seems commercial fuel cell efficiencies are around the 60% mark (minus electrical losses) with room to improve. Modern jet engine thermal efficiencies are generally around 50-55%. So yeah fuel cell probably could win but would essentially require re-engineering the entire propulsion system. Faster/cheaper to just adapt and recertify exiting engine designs and focus all that engineering effort on designing/certifying aircraft to carry cryogenic/10,000psi hydrogen tanks!.