The first couple had to run bcoz of the emperor which sucks plus it was human+sword rather than human/human or sword/sword. Mikoto and Shiou were in my opinion not really a couple (except at the very end when Shiou finally grew some b...s) as they came together due to "human" interference/manipulations/plots. But in the end Ninomaya/Nanaki are my favorite although Nanaki is a bit of a cry baby. ShenJin/Toranasuke are a close 2nd-but they are not swords. But i agree the 1st couple got a shitty deal but at least they are together! And u r right...it is a superb read!! All three volumes!
I hate the fact that the first pair had to run away and the others don't (which just encourages me to say that the second pair are a coward(only the uke though). Except for that-everything is superb.