- Maximals morph rather than transform
- Once the Maximals learn to morph, we find that their robot modes have funky energy redirection or tasers or swords instead of any kind of traditional Transformer weaponry, which further distances the techno-organic characters from the Transformers legacy
- Transformation being equated to spirituality kind of sucked
- Terrible character arc for Rhinox--resurrected as an enemy, regains memories, STAYS an enemy for completely uncharacteristic reasons, and ultimately dies a psychotic moron (I still attribute it to his Vehicon shell program corrupting his mind, regardless of what Bob Skir or the other writers claim)
- Badly executed character arc for Cheetor--instead of showing him maturing and becoming a logically challenging voice to Optimus' leadership as intended, he's portrayed as whinier than ever
- Terrible, angsty character arc for the previously fun Silverbolt--his answer to enjoying being free of his code of honor as Jetstorm is to continue to ignore his code of honor once his mind is clear, drive Blackarachnia away, and occasionally endanger his supposed friends
- Rattrap has no legs and generally looks stupid in robot mode
- Nightscream... I'll just leave it at that
- Savage/Noble beast-to-beast transformation (and the character in general) was lame
- Megatron becomes a bit of a joke in the second season, jumping from body to body and generally being kind of useless
- Strika and Obsidian were boring non-characters with very little personality or charisma, unlike the unique, varied, and, most importantly, fun villains of Beast Wars like Inferno, Rampage, Quickstrike, et al.
- Automatically portraying techno-organic as better than purely cybernetic for no real reason was a bit stupid