I think the use of the word destiny is strong language. It implies a singular result from inception to infinity. Any true system will evolve or change over time to fit the needs of the environment, or in this case its users over time. The only constant is change.
To your points...
tag suggestion system is a touchy area. There are millions of users with their own work flows and styles. Any suggestion system implemented may work for a few, but then generate complaints it doesn't work for everyone else.
I don't see any issue with changing the date created on the desktop apps, perhaps more explanation can be provided?
capturing the creation date could only support one source, that would be the file creation date from the system OS. Doable, I could see this as a feature.
What constitutes a duplicate? Your definition of a duplicate can easily be different from another user.
Your use of Evernote is different then others. You use it as a document storage and retrieval system.Others user it for notes. And others use it for task management. In all, these are the functions users have designed into Evernote for their needs. Evernote is a framework, and you build on that frame work.
One of the problems with trying to implement features to please everyone is running into the Microsoft syndrome. Microsoft tried to implement features in their office products to try to please everyone. But it became to bloated, it developed a reputation for being slow, clunky, and bug ridden. Microsoft has turned that around. Evernote can't fall for the same trap.
Honestly its sounds like you need a dedicated document management system you can customize.