Tuma and Sidorak both irk me for the same reason. I don't mind puppet villains so long as they convince me(Bane from the Dark Knight Rising's a good example), but these two didn't do anything before being dispatched by their respective manipulators.
They were played up in media, but not so much in tangible story so it came off like the Bionicle team was trying to fool the audience rather than the in-universe characters. Sure, optimally you'd trick both the audience and the characters, but if you're only going to do one, do so in universe. IMO it should be a surprise that the big bad was being puppeteered, otherwise they weren't an effective pawn to start with.
I'm not sure if that gets my point across well, but hopefully you see what I mean. They didn't make any real impression as villains, so it just felt like they were in-and-out puppets with 19.99 pricetags.