"Shit got fucky" around ~2005, but "shit getting fucky" is Doom Patrol's entire thing. I haven't read the Pollock stuff after Morrison finished, but I think Cliff was working with the Chief in that, though the Chief was just a disembodied head.
After the Vertigo series ended, John Arcudi started a volume in 2001 (which I haven't actually read), in which he used a mostly new team. He used the excuse that Dorothy went nuts after Pollack's run and accidentally killed the old team, and then became brain-dead. The series wasn't a success, and was cancelled after 2 years.
In 2004 John Byrne decided to do a full reboot of the series because "backstory got longer and more complex" for new readers. He did this by ignoring that Beast Boy was being used by Johns in his TT book, and suddenly Gar no longer had any family or connections to the Doom Patrol. Byrne even mentioned that in his column at the end of the first issue (see attached), but he clearly didn't give a fuck because he could bring back the "younger" Rita that he wanted. This reboot was not considered good by readers (it's basically just x-men), and Johns decided to work around Byrne. When Superboy-Prime punched the walls of reality in Infinite Crisis, Gar being the adopted son of Rita was one of the things that got reverted. I'll try to find the page of them remembering their relationships with each other.
So, as for why everyone is working with Niles, part of it can be blamed on Byrne wanted a new status quo, and then Johns trying to reinsert some older canon. It doesn't really matter though, because when Kieth Giffen had a new volume a few years later, he ignored most of the stuff that Byrne did (by killing Byrne's OC's in the first issues), and had Niles be a head again.