Out of all the canon B5 books (To Dream in the City of Sorrows, The Shadow Within, the Psi Corps trilogy, the Centauri trilogy, and the Technomage trilogy), the Centauri trilogy is the only one I've never reread, which should tell you what I think about it right there. You are right to notice problems in the books, the biggest one for me is how there are about six months or so in between when Londo becomes emperor, and the final episodes of the show in 2262. From what I understand, Peter David got information with the wrong dates.
The books just really didn't do it for me. I thought that Galen's manipulation of Mariel's emotions was totally out of character, even when I read it back then when all I had seen of him was A Call to Arms and Crusade, and with how we learn more about him from the Technomage trilogy, it's even worse. I just cannot see Galen doing that. I really felt that the trilogy was a wasted oppertunity. It was one of the most interesting points in B5 history that wasn't shown in the show, and I thought it could have been much better.
The Psi Corps and Technomage trilogies though, were real SF books that I would still think were great even if they didn't have the B5 connection. I really have to say that I prefer how the technomages were depicted in Jeanne Cavelos's books than how JMS has shown them.
I seem to remember other things that were wrong in the Centauri trilogy, but I've never reread them (except for a few sentances maybe every two years or so to do some fact checking when talking about B5 stuff), and I only read the books once, while I've lost count of how many times I've read the other B5 books. For me, I'm not sure if I like the Psi Corps or Technomage books best.
Of course, it is true that there are mistakes I noticed in the Psi Corps and Technomage books as well, but I'm more willing to forgive them since I thought they were written so well. And if there were ever a series of Crusade novels released to finish it up, my top choice for that would definitely have to be Jeanne Cavelos.