What's most interesting to me is to look beyond the surface similarities to think about what Bakker has done differently with these elements.
For instance, there are obvious similarities between Nonmen and elves (come before humans, teach some of them who are thus raised above the others, immortal, their civilization waning as humanity waxes, twisted by the Big Evil into orcs/sranc, etc), but the differences are what fascinate me. In Tolkien, the elves, with their immortality, are kind of the wiser, more patient "big brothers" of humanity. While the Nonmen do teach humanity, they also inflict a terrible slavery on them, whether the pits we see in Cil-Aujus or the Emwamma. The thing that struck me first and hardest, though, was the effect of immortality: Nonmen aren't "wise" so much as alien to us; and, of course, they end up being driven insane because of the way that memory degrades over the course of a lifetime. Even their propensity toward betrayal, especially when we're talking about the Erratics: it's like their long lives make the lives of others inconsequential, just a tool to be used to spark their memories.
Or how about Achamian vs. Gandalf? I like the analogy drawn between him in The Aspect Emperor and Gandalf in the Hobbit, but of course it's the differences that are striking. Gandalf is genuinely interested in the success of the quest, while it's a tool for Achamian. In fact, Gandalf genuinely cares about the members of the party, especially including Bilbo, who is basically sent along for his own personal growth. There's a benevolence there with Gandalf, who additionally is kind of "above the fray" and also a bit of deus ex machina with the ways he leaves and returns. Akka, by contrast, has to be saved more often than he saves the party, despite the fact that he does indeed have incredible power at his command. And although it pricks his conscience, at the end of the day he's using them as an ends to achieve a means.
(Thorin Oakenshield and Lord Kosoter, though: pretty much the same.)
Staying with Akka, take him back to the first trilogy. There's a certain similarity between him and LotR Gandalf as well. They're both out to save the world, with deeper knowledge than any of the human characters have, they're both, to some extent, doubted by the powerful, and obviously both wizards. But Gandalf is this sort of wise, knowing guide and mentor who's not QUITE always right, but he's certainly always GOOD, he's always motivated by a higher purpose (he's sent by the Valar to help men and elves, and he remains true to that mission). Compare that to Akka: yes, he's basically a good guy, but he's full of uncertainty, full of mixed motives and just generally a lot more HUMAN than Gandalf ever seems to be. He screws up his personal relationships, he screws up his world-saving duty... we have to be reminded every so often that he IS actually a total badass, because he doesn't show it all that often. Anyway, all of that plays into the differences in the kind of story Bakker is telling. Clear good and evil vs. a very muddy morality. Authority figures who can be trusted to there being very few real authority figures, and each of them having an agenda.
Anyway, just some off-the-cuff thoughts.