I have a soft spot for the Jade Phoenix trilogy, though I can understand why people might not like it. And I think it does have flaws - the pacing is odd, so that the story feels very disjointed at times. I think it could definitely be better written. But I also think it is, in its own way, superior at least to Thurston's later BT books, some of which really came across as the token 'Jade Falcon' books (at best - Freebirth in particular deserves a good kicking... my brother had never been a big fiction reader, but I'd introduced him to some of my BT novels. He screamed through the Warrior trilogy, the BoK trilogy, some of the later books, got onto the Twilight of the Clans series... hit Freebirth and never got any further... but that's another story!)
Anyway, I think the protagonists and main characters in the Jade Phoenix trilogy are pretty unlikeable, but I think that's deliberate. Because the real character of the trilogy is the Clan system itself. As mentioned, they're our first real look at it (and that in itself I think makes the trilogy more than filler), but they're also dystopian novels, because it isn't pretty. We're not meant to like the Clan system, because as we're shown it's monstrous - it abuses young children and teaches them to kill, it routinely denies the value of human life, and above all has deliberately excised from life some of the most fundamental things that make us human, such as family and love and compassion. And all the Clan characters in the novels are damaged by that system. The fact that Aidan's book collection is not only secret, but also illegal is a classical element in dystopian fiction, but this is a dystopia that's been in place long enough that now noone can even understand the banned elements - Newspeak has been in place for a long while. I think Thurston's later books are weaker because, in part, they seem to actually buy in to some of the propaganda and forget this dystopian element, but it seems pretty deliberate in the Jade Phoenix trilogy itself.
And Aidan's character shows that. As Rtif's points out, the main point is that he's not this great reformer throwing off the iniquities of the system. He's also indoctrinated and stuck in the Clan way. Horse calls him out on various things like the seeking for a bloodname, and I think it's actually a strength that the story has Aidan unable to articulate why those things matter to him. But at the same time, his experiences and his reading and his character leave him standing out, seeing this other stuff but (due to his indoctrination), unable to grasp it, but also unable to leave it alone. And so he's in this odd position where he can see on one hand how the Clan is failing to live up to its own ideals, and on the other is experiencing these very unclanlike thoughts in his head. And I think it's a crowning irony (whether intended or not), that he gets all these honours at the end for what is ultimately an extremely unclanlike act for a warrior. Because in the end he doesn't die for his clan, but dies for his daughter.
Could all that have been better executed? Definitely. They could certainly have been better written. I wouldn't place them amongst the best of BT fiction, or amongst my personal favourites (probably Exodus Road and The Last Charge). But I think they really deserve a place above a lot of the more generic stories because they're doing something that a lot of the others simply aren't doing.