Food and seating in KE is superior to CI, in all classes of service. Connection in TPE or ICN is good in both (both are fine airports, though TPE T1 is kept a bit too warm with very weak or no AC, unlike T2 that always has a comfortable temperature and much better AC, and T1 at TPE is still undergoing renovation as well), but if it's long enough to go and see the city, ICN is better as there you can take a train direct to Seoul centre (in TPE would have to take a rather pricey taxi at 1300 TWD one-way). So unless CI is a lot lower price, and/or unless the KE fare earns no miles, I'd say go with KE.