The prequels are really the story of the arrogance of the Jedi Order allowing Palpatine to steal their Chosen One right out from under them. The Bane books were released shortly after the prequel trilogy (2006-08), and I think they are influenced by the very best of Lucas' storytelling in the prequels. Besides Bane being generally awesome, I thought Karpyshyn did an excellent job portraying the grayness of even the best Jedi in the period before the High Republic era. The leaders of the Jedi, like Lord Hoth, tap into the dark side to gain strength, but they don't lose themselves in it. This is also how I saw Luke in the original trilogy - he still loves his friends and family, and his passion lends him strength - he certainly leans into the dark to overpower Vader in their Death Star duel, but it doesn't consume him.
But the Bane trilogy sets up the Ruusan Reformations, which reduce the size of the Jedi army and leads to the ostracization of the veterans of the war. The reformations create this stigma around grayer Jedi, even though the grayer Jedi, like Qui-Gon, Anakin, and Luke, are some of the strongest Force users. In the prequels, the Jedi try to insist that the only way to use the Force is to tap into exclusively the light side. But the Force has always had darkness within light and vice versa. The Jedi forget this symbiosis in the aftermath of the Bane trilogy, and it leads to them alienating Anakin when he is expected to blindly believe their half-truths. After all, how is the Chosen One, the person who is supposed to bring balance to the Force, supposed to do that when the Jedi don't allow him to understand the dark side? No wonder it was so easy for Palpatine to corrupt Anakin. So, even though Anakin sucks sometimes, I always enjoy watching the prequels.