My thoughts on some of this..
Permissions - not sure what you mean here, you can set the permissions for each user category already.
Pages - The "Questions" page lists questions in order by newest. The main page shows activity except comments and all activity shows everything. If anything should be called "main" it should be all activity. You can change the titles using the language file (qa-lang-main.php I think)
Spam - You can limit per hour so just divide by 24 i.e. if you don't want more than 24 per day use 1 per hour. Maybe you want less that 24 per day, but one per hour protects against spam which is always based on "do as much as you can before the admin notices and deletes/bans you". So after one question they'd go away and not come back.
Points/Reputation - no idea what you mean. If reputation is the numbers they get from votes, what are points? They are the same thing.
There was a question before about asking questions to specific users. This really goes against the Q&A principle in my opinion and alienates other users.
The other suggestions seem quite good. Some of them will be able to be added as extensions when the next version comes out.