[MENTION=11786]Sweet J[/MENTION] No explanation on where Darla and Luke are, they've always been with the Master, they wouldn't just up and leave. Angel killed Darla to save Buffy. No Buffy = no reason to kill Darla, and Luke was old enough and strong enough to defend himself against Giles and his men.
Why would the Mayor let the Master gain so much power so close to the Ascension? He wanted Spike gone as soon as he came back to Sunnydale in season 3. No way would he let the Master and his men run the town.
Where is the Initiative? They didn't just pop up out of nowhere, their underground lap would have taken a long time to build. Riley and his men would have taken down The Bronze come daylight.
Angel died. Angel is destined to become a champion and play the deciding role in good vs. evil. He has to for fill the Shanshu Prophecy, plus Connor has to be born so he can for fill the prophecy of killing Sahjhan. Sahjhan knew Connor was the one to kill him, which is why he spent most of season 3 trying to get baby Connor killed. Anya's wish wouldn't have changed what Sahjhan learned about his future.
The Wish took everything and threw it out the window. Personally I like to think it's because the higher powers knew that any and all spells done to create new universes would be undone and wiped from existence. They see past, present and future. If any wish from a mere vengeance demon were to upset their plans and balance of the universe they would have stepped in and took control of the situation. But still, I think it'd be best to just avoid making those inconsistencies in the first place. As much as I loved "The Wish" and Vamp Willow I wouldn't want to see her or that world again.