Are all weapons allowed? What's the setting in which they fight? Ayame is generally involved in sneaky, ambush battles rather than "Have at thee!" type duels.
Yes, the boss fights were like that. The typical MO for the Tenchu ninja was sneak around and stab though.
Anyways, I'd like to give Ayame the edge. She seems more experienced overall. She's also got a few more tools at her disposal if items are allowed.
However, I wouldn't count Kaede out. She was trusted enough by the Iga clan to be sent after Samanosuke. Going by gameplay(she doesn't have many feats), she is about as physically capable as Ayame as well.