I think you've got some good points Tarik. Something I'm starting to realise is that there is necesaarily some cooperation from uke, as after the first throw (when you're training) they know you're going to do the same again - and therefore block it if they want to.
However most people that attack you for real don't know what you're going to do (thus the ability to work on your opponents reactions to an atemi), and you have the option of doing any technique (or indeed anything, including strikes), so they can't really block it - cos you then do a different technique.
It is very unfortunate that, to train in a formal way we have to go through repeated techniques of one type, whereas ideally we want to be changing our technique every time to respond to that particular uke and that attack. How do we simulate this? Possibly a lot of it is attitude? Possibly just later on we have to develop the fluidity.
Don't ask me I'm still wrestling with this one.