In the Government's mind being "permissioned" allows you to come to the country and begin to get used to it, being a "probationary" Citizen allows you to prove your "worth" to the UK.
All of your points are part of the concerns we formally presented to the larger immigration advocacy community and which actually made it into the briefing pack that was presented to the House of Lords before the bill was presented to them. While several of the Lords were very sympathetic to our concerns, it is hard to say how much will persist into the final bill. Pop over to the Advocacy section of the forums for some details and you can keep an eye on any actions we take as a group.
I totally agree that uncertinity, especially in the world today, makes it almost impossible to plan a secure and safe life for us and our loved ones and then when we are charged an ever increasing premium for the "privilage" to settle in the UK, it becomes ever the more difficult, but right now, it is totally safe to be "hard on immigrants". No one is going to lose office based on that. Sad but true.