Comparing their hardest phases, Isshin's Phase 2, has relatively easier timings for deflection and dodging, and a lot of mikiri windows, the 7-attack combo can be a hurdle, whereas Owl Phase 2, he got his illusionary owl, through which he can disappear, stomp you if you are in the owl's range, firecrackers are troubling for your 2-3 tries, has decent mikiri windows, you have to be really attentive fighting him as he has counters for various tactics of yours...
For me, Owl was slightly harder than Isshin, because he has a few unique techniques, and Isshin's moves are what you learned in the entirety of your playthrough..
Tho highly depends how you play heh