Phantoka and easy to break pieces, even though they looked really cool, they were cheaply manufactured sadly.
The ending: it was rushed, and I know it was supposed to be cooler and longer, but the end was handled badly, mainly set wise. Story was ok, it would've been better if Greg got his way.
I see the lack of female characters debate and I agree, there could've been more.
Also, then end of collectible masks, or at least when they ended. I think it would've been cool if they ended with the toa metru, cause imagine how cool variations would've been on those masks.
Lack of change in the last few years of bionicle. Keeping over all the inika build, which was a great build, but if they could have shifted away from that to something more original, that ould've been awesome.
Squid launchers. HOW DO THEY EVEN WORK?!?!
The movies: WAIT! before you freak out, I enjoy the movies, but honestly, they could've been animated better, like how they did the commercials? imagine a bionicle movie with that cool animation. and maybe less cheesy...
And while this doesn't bother me, but it might've worked better if these were all black, but the multiple colors for the pins and axles? I think just black would've been cheaper and look nicer. But hey, only a minor thing to me.
The fact that certain characters didn't get sets.
AND FINALLY, I've already brushed this, but the final wave of sets. They made me sad inside. Though, I did like the bringing back of two kanohi.
OK that all being said, I still freakin' love Bionicle, I was just tossing the only flaws I could think of. So... yeah.