There are 2 that stick out for me - both around season 7 - that annoyed me at the time and in re-watches.
The whole story with Peter's mother Sylvia, was really tedious and didn't really go anywhere. First she was his mother, then she wasn't, then they were trying to get money out of Greg, then was Peter trying to poison her? I never cared about her or the storyline but Ruth Roman had loads of screen time that year, but then it all fizzled out. And nothing ever really came of Peter and Jill being siblings getting revenge on Sumner for swindling their family. They never did get revenge and that plotline got forgotten after a while too.
The other one is Empire Valley and that John Coblenz character, which is kind of linked as well. That story was retconned so many times it was difficult to keep up. One week it was a massive real estate development, then it was a secret government intelligence complex, then a toxic waste dump,. Gary going undercover for Coblenz was a real nadir. I found Coblenz extremely unconvincing, he looked liked Bryan Ferry's wicked twin. And didn't Galveston leave Empire Valley to Gary because they bonded and he saw him as the son that Sumner would never be. Why would he have left it to Gary if it was all polluted?
I think the writing teams had changed midway through season 6, and this story line just got as toxic as the Lotus Point reservoir. Of course everyone remembers the masterpiece storyline of this period - Val's babies which was mostly excellent throughout, it's easy to forget there were also some really crappy sub plots thru seasons 6-7 too.
No I won't mention Jean Hackney and season 8....