1999 was the year Nicole started to become more interesting. First when she married Lucas, and then later when she started drinking. Arianne Zucker's acting also improved when she started working more with John Aniston and Lauren Koslow.
Sami and Celeste plotted to kill EJ. I know in one of those last episodes that featured Penthouse Grille EJ was taunting Celeste about Lexie's disappearance. And of course there was Shawn and Belle hiding on Tinda Lao from Philip.
I said this a few years ago but I think someone higher up was also obsessed with Daniel/Shawn Christian. Maybe Corday, or someone at NBC or Sony. Of course the different writing regimes also worshipped him, with TomSell being the worst.