Interesting to ponder. I think to a large extent my preferences vary from one volume to the next; different authors handled certain characters differently.
If I'm looking to generalize, though, I always really liked Desai. She seemed to have a serious, principled set of ethics that made for thought-provoking contrasts with events around her. It was disappointing to see her role diminished so much as the series progressed.
Conversely, I really never warmed up to Reyes, no matter who was writing him. To be honest, this caused me some frustration with the series overall, given how central he was. Basically he just came across as an arrogant, antisocial, authoritarian prick, with an ends-justify-the-means sense of ethics. Not exactly an example of Starfleet's finest.
Perhaps if the series had spent more time exploring the irony of his prosecution — namely, the fact that he was put on trial for arguably the most honorable thing he'd done, letting a free press disclose important information that shouldn't have been classified in the first place — I might have found him more interesting. Unfortunately, that development really only seemed to be used as a plot device to get him off the station for a while.