I think there are a lot of misconceptions about how involved Joss always was in his shows. Of course it's by the fans that didn't like something like the darker Season 6. It was really life that was the big bad that season though. That was just one thing that was different on the show.
One of the biggest reasons BTVS was such a success is because for the most part Joss is an amazing writer. He was also lucky to have a great writing team and of course the incredible actors. In the end Joss always had final say for everything. That's partly why some shows thrive and others don't. I could give examples of others but that would make this post longer and some may disagree. Yes Marti became a big factor in the show with her ideas.
If Joss didn't like it he would change it. He wrote the musical. That was one of the most important episodes of that season and show. We saw all the issues that would eventually come to a head at the end of the season. Well except things with the nerds.
Well most of what I know that was Joss influence is about Spuffy of course. I do know that killing Tara off was his idea and was supposed to happen Season 5 and for Willow to go evil then. I think I read that Anya was supposed to die in The Gift too. I don't know remember how though.
The Smashed ending with the crumbling walls and Spuffy bring down the building the balcony scene in DT was also his idea. He wrote the scene in HB when Spuffy talk at the wedding.
The most major rewrite I know is the BY ending when Spike tells Buffy about his soul.
Any way obviously the show wouldn't be So well written if it wasn't Joss that created and stayed with the show it's entire run. That is another thing that hurts shows when the creator leaves.
One of the reasons I blame Joss for the mess of Season ATS is because that is when he gained complete control and David Greenwalt left. No one is going to write perfectly and have the best ideas all the though.
I'm tired of typing this and it's already longer than I meant for it to be.
There is more I know about ATS that I will post about later.