2 for me, for me (meaning opinionated):
1) Faith jails herself in an institution where she can break out of, and has done so in Angel. Why? How does a false prison help her? Especially over staying on Angel's team in the Angel television show? So, THE Slayer is put on the shelf for whatever reason (whether it be actress/creative issue). In an institution which has no way in aiding the young, super powered, mentally ill, woman's mental health....WHAT?! This is the best we get for one of the key, if not THE key players/reasons why S3 can easily be called the best season of Buffy? (along with S2, at least from the polls that I've looked over. Yes I think Faith and the issues/fallout from her character, coupled with the Mayor, is the reason why S3 is so great.) I can understand if you need to shelve Faith, but the way she was put on the bench is stupid.
2) Spike's character in it's totality is the stupidest fan service 'good guy', or 'baby face' turn i have ever seen. Goes from a cool badass, a soulless 'monster' who plays by his own rules, to a Slayer/human's bi-- you know what. For some reason, a vampire without a soul is chasing Slayer tail. Not to only get in her pants, and i say that to romanticize that idea, but to eventually be in a relationship with her. Even to go so far as to seek out a soul. Why? Spike's character change/development turns me off to his character completely, in Buffy anyways. In Angel, whether you think i'm wrong or not, i treated him as a separate entity/being/character from the Buffy show. I've seen many arguments for why Spike is different, and have been shows examples of why his character development is possible/acceptable. And i. don't. care. I still find the idea and process of how Spike went from evil to good, stupid and a complete fan service.
Again, just an opinion of a an average Joe. Put the stones down.
cheers