I've never really cared whose fault it was. The show is a mess.
If I blame anyone, it's whoever wanted 26 episodes in the first place. Beast Wars season 2 was able to tell a good story in 13 episodes, but it was only able to do that because season 1 had 26 episodes. Those early "filler" episodes (I hate that they get characterized as such) were immensely important. They let the writers explore and develop the characters and setting before building up to the big events. A 13 episode season 1 with just the plot episodes would have ended with a Rattrap that's either still a jerk or stopped being a jerk way more abruptly. There's a lot of little things like that.
Maybe the Beast Wars crew could have made a good 13 episode season 1 for Beast Machines, but a new crew deserved the same chance to get a handle on things before they tried their big ideas. Beast Machines has a ton of interesting ideas but season 1 burns through them about as quickly as they're introduced. We've barely met Tankor before they drop the very heavy hints that he's Rhinox. It's too fast. On the other hand, it manages to be repetitive, which is quite a feat for a serialized 13 episode season. Megatron starts out interesting and menacing, but he becomes hard to take seriously anymore once you notice the Maximals are visiting his house every other night and safely leaving.
It's also obvious that the writers needed more time to talk to each other and make sure the Maximals didn't have wildly different memories from one episode to the next. To be fair, this is much more obvious on a binge watch than it was at the time. But still. They wanted to tell a tightly serialized story but also winged it.
And the endgame is still stupid no matter whose idea it was. Cybertron has been completely conquered, the planet is patrolled by nothing but drones guided by a single mind, and the solution to this is... dirt. Really. That's what's wrong with Megatron's Cybertron? There's nothing else wrong with this picture? The inhabitants of Cybertron have been ripped out of their bodies and imprisoned, and the alternative to this is that they need partially fleshy bodies instead. Obnoxiously ugly fleshy bodies. This is what's needed. The only possible alternatives are a planet running as a single pure machine with no free will, and a technorganic planet with seemingly deliberately hideous inhabitants with free will.
No. The series does not make it even slightly clear why its technorganic endgame is a good or needed step in Transformers evolution. Take G1 and Beast Wars out of it. It's not really fair to look at a sequel completely in a vacuum, but let's pretend that it's fair. You do not need to care one iota about G1 to not like Beast Machines' ending. It fails to explain why you should like it. It's simply not justified that this is the only alternative to Megatron's single elegant machine. It was possible to be a mechanical Cybertronian with free will before Megatron took over. It is possible to be handsome mechanical Vehicon with a spark and free will, aside from the safequards Megatron added. It is possible to be a mechanical diagnostic drone and have a seemingly full range of personality. The technorganic revolution is not evidently needed to fix what's wrong with Megatron's Cybertron. It's a tangent.
This is not how to write a series. There has to be some reason to want what the heroes want. Beast Machines' attitude is "Just want it because the Oracle wants it." Okay maybe the Oracle does know but the problem is I don't. In Beast Wars I wanted to see the Maximals make it home because I cared about them as characters. In Beast Machines I'm supposed to want them to bring about the technorganic revolution because their supervisor says so. You're not my supervisor.
