I always thought this design was poor, as were the many continuity issues in WC3.
I guess I should read the script carefully to come to a real conclusion, but my impression so far is that WC3 has some "this seems cool, so let's write it this way" storylines.
About Thrakhath: After I read the Freedom Flight and WC2 script more carefully I felt that the character of Thrakhath actually had more depth than that was in WC3. Yes, this character is a villain one, but not a mad one. He had his own troubles, hurt feelings, and selfish interests independent of the empire.
As for Ralgha, the situation is even more complicated. His leaving the Empire to join the Resistance was a complex political outcome. For example, as close relatives of the emperor's clan, all of Ralgha's family (and most of his close vassals) was destroyed in an "accident", except for Ralgha himself and the young vassal Kirha. Considering how the emperor and Thrakhath described Gilkarg's "accident", isn't there room for thought here? And from Ralgha and Kirha's mere words related to the emperor's family, Ralgha and Kirha showed no kindness to either the emperor or Thrakhath.
All of the above illustrate the complexity of the internal contradictions of a feudal empire, a state of politics that is actually common knowledge to us. And all of these was not much reflected in the WC3 game script. BTW, Melek's depiction in WC3 novel is more interesting.
That said, it is at least debatable whether the series has really paid attention to the issue of continuity since WC3. There are so many discontinuities from WC3 to WC Movie that seemed to be caused by random ideas.