MVC

Current SC structure and model is against any kind of integration.
Anybody knows what are the chances that SCriptcase will finally separate PHP, HTML AND CSS to follow MVC model ?

Doubt very much it would be on their priority list. Purpose of MVC is to help you organize your code for easy readability and maintenance. SC is a generator which has compartmentalized your code in another readable/ maintainable way.

IMO for that to be possible (MVC), they would have to start ScriptCase from zero…

I think that all is still based upon the codebase of 10 year ago and migrated into the current version. So I agree with @marmede. It would require a total overhaul.