I thought the entire Thel 'Vadam (The Arbiter) story converging with Keyes' was amazing... as I'm sure you can tell, a large part of my interest in the stories is from the Covenant side.
Really fed to the way I see Thel's character progression, and seeing him in his prime was awesome. Really enjoyed that bitchy Jackal rebel leader Reth was an oddly memorable character. Having Thel sent by the Prophets to kill him seemed to be quite an ominous piece of foreshadowing for what eventually happens in Halo 2. I need to give it another read, but there we some other very interesting Covenant characters in there as well (and dat ending).
The UNSC story also worked well for me (undercover Spartan operatives get in a bar brawl on a Rebel asteroid station, need I say more?), with some fantastic insight into what really drives Keyes, showing him on a much more relatable level than 'Captain Army Man Extrordinaire'. The ship to ship combat jargon was also kept to a minimum, and everything moved at a wonderful pace, with tense situations always ready to come and mess up the character's days, be they human or Covenant.
So that's why I loved The Cole Protocol.
