hmm, well i have two views on that...
gameplay: for me, Xehanort's Heartless was harder, mainly because i tend to skip the random battles a number of times, so i was low level take out him. that and by the time i fought Xemnas, i had more exp (with playing the game, not Sora's level).
storywise: xemnas, for a couple of reasons. in KH1, there is no sign that Xehanort's Heartless caused near death of Sora (aside from possibly his falling into the abyss towards the begining). Xemnas's fights, Sora and Riku are on the verge of being beaten at the final battle. also, take into acount that Sora is stronger then than his KH1 counterpart, we can say that Xemnas is stronger than Xehanort's Heartless was.
with all due respect,
Merlin326