Time Trap was released in 2005, and Hero Factory didn't launch until 2010. Are you sure that HF's story was written that far in advance? I find your use of the word instead to be interesting, since Greg continued writing Bionicle until 2011. Next, Bionicle has always been a side-job for him. Greg's primary job was writing for the Lego Magazine and other material for the company. At no point in his career with Lego was his effort dedicated 100% to Bionicle.
I still have no idea why people hate Teridax so much. Yes, I can kind of see how it diminishes some of the mystique to character, but it honestly never bothered me. What bothered me is the people who went on vicious tirades about it. It's not a big deal at all. Anyway, about the brothers deal... when the story was first written, Mata Nui and Makuta were considered Great Beings. The equivalents of the embodiments of good and evil (or creation and destruction), with equivalents being the operative word. Not too much later on, as the story evolved, it was confirmed that they were "brothers" in that they simply worked together. This was "explicitly established" in like 2003. Mata Nui was the equivalent of the somatic nervous system, controlling the outward actions of the Great Spirit Robot. Makuta was the equivalent of the autonomous nervous system, making sure everything was running smoothly on the inside.
Next, Greg never ran the show until after Bionicle's cancellation, when G1 became nothing but online serials. Up until that point, he was just one person in a team of about 5 or 6, and he was at no point the leader. He was just the writer. They all worked together to come up with the plot, and Greg's job was to turn it into something readable.
Are you talking about the Nuva and Inika? While it would have been nice to see the Nuva back in action a little sooner, 2006-8 was great for taking the story in a really new direction. New heroes means you get new powers, new personalities, and new solutions to problems. If we had the Toa Nuva all the time, things would have been way too predictable. You'd get sick and tired of Tahu and Kopaka's bickering and you'd be begging for some new Toa to come around. Also, which one of the Inika was even an anti-hero? Matoro? He was reluctant; he felt that he wasn't qualified to be a Toa, but that's not what an anti-hero is.
Are you talking about the Federation of Fear serial? That was just a side-story that largely existed as fan-service to see some old favorites back in action.
Like I said earlier, Greg was never in charge of where the story went overall. He was only one member on a team where everyone had roughly equal say. Also, the 2006 story bible was probably locked down before Time Trap was actually written.