All these are not an issue at all. I beleive with View 5.0 you will not able to create an individual desktop. That is an old concept. You might be created a manual pool when one Vm source in it.
1). When I try to connect a VM from the client it asks for certificate....why?
You need to configure certificate for your Connection servers. Also you need to intstall root CA certificate in client as weel (if not present)
Refer View administration guide/ deploymen guide for Certificate configuration
2). when the agent machine (A) is logged in through administrator, i try to connect from client (E) by user1 (entitled), I get an error that there is a connection already exist "please try after sometime, however there is no connecting at that moment.
All desktop operating system support only once session to the system at a time. For a user to connect from View client, local console session should not be present. (You can see this in "sessions" tab of view administrator)
3). If the agent machine (A) is logged in from user1 and I try to connect from client machine (E) which is also logged in from user1, when the connection initiates it gives some local policy error and asks to connect from administrator and if I try to connect from administrator it gets connected.....why?
Please ensure that there are no console logn to agent machine, so that it can be launched from View Client
