I miss the user contributed notes. I miss the way you can drill down on the left hand side of the screen. I miss the multitude of quick examples embedded alongside the documentation (py docs has some but not nearly as many). I find the descriptive language used more approachable and easier to understand. I also prefer the general look and feel.
To answer your second point about deployment: regarding your ini file, you set this up once how you want it to be and then use that across all your projects. Not very hard. As for apache, I don't know what you were doing but in my experience it's almost impossible for apache not to find php. I've just setup uWSGI (plus emperor) + mongrel2 + Flask (in a virtualenv) and that is 100 time harder to get going than apache and mod_fcgid (IMHO).
To answer your second point about deployment: regarding your ini file, you set this up once how you want it to be and then use that across all your projects. Not very hard. As for apache, I don't know what you were doing but in my experience it's almost impossible for apache not to find php. I've just setup uWSGI (plus emperor) + mongrel2 + Flask (in a virtualenv) and that is 100 time harder to get going than apache and mod_fcgid (IMHO).