Something that a lot of folks may not know is that a lot of the things people disliked about Beast Machines came not originally from Bob Skir, Marty Isenberg, Marv Wolfman, or any of the people making the show, but were instead the wishes and mandates placed upon the show by Hasbro itself!
As stated in these videos:
According to what Skir said in these videos, Hasbro wanted BM to be all spiritual and religious, which Skir was initially against and tried to talk them out of it, but they kept insisting. He came up with several ideas that he thought would have snapped Hasbro out of their craziness, but no, they kept liking and approving those ideas that led BM to be "a religious epic novel for television". Skir was sure they would eventually change their minds and realize how nuts they were sounding, but they didn't and he did his best to give them what they wanted.
It was even Hasbro who wanted Beast Machines to be, and I quote, "as much of a departure from Beast Wars as Beast Wars was from the original Transformers shows," like a fresh start soft reboot to better enable new viewers to jump on. And, Hasbro wanted to do something different at the time. "If you're going to rethink something, rethink it differently," is what Hasbro was thinking back then. This is why Hasbro brought in new people for BM instead of keeping on Bob Forward and Larry DiTillio.
The character designs were likewise made outside of Skir's control and without any of his input. When he was writing episodes with what he was told about the characters in mind, he hadn't yet been shown the character design for Rattrap until about five episodes into the series. And when he was finally shown what Rattrap was gonna look like... he didn't like it. He felt that Rattrap's BM design was so goofy-looking. In fact, he says that it was even designed to be goofy on purpose: "What Asaph Fipke said at the time was they wanted to give this tough-talkin' guy a really really goofy robot mode," and that it was completely counterpoint to what Skir was writing up to that point.
Same with Nightscream. He'd created the character as a John Connor type, but when he finally saw the design, he felt the "ankle wings" look made him look too much like a skateboarder. And yet, these were the designs that he had no choice but to work with, since he had no say on the matter.
Hasbro even at one point asked Skir to give Beast Machines a
third season (which I guess would explain why there were so many toys at the end of the line that either never saw release or were carried over into RID'01; Hasbro was probably hoping for one more year to release them). But Skir put his foot down on that one and said NO! Beast Machines had been pitched as a "26-episode novel for television". He knew at the time that some fans loved it and other fans hated it with a passion, and felt that a third season would be a disservice to both the story and to the fans on both sides. Skir would have had to pad out the story in order to drag it out into a third season, and knew that doing so would have upset both the fans who liked the show and the fans who wanted it to end. Two seasons was the deal and he didn't want to make it twice as longer just for the sake of making it longer.
He talks about much more in that third video, but the above is all the stuff relevant to the things that Hasbro mandated to the BM writing staff.
EDIT: Digging around, this old
FAQ from 1999 further mentions Hasbro's insistence on adding the spiritual stuff to the show.