Cubase in my opinion is excellent, but creating a new project disturbs me. When you decide to save your new project, or rather using the Save As option, why does Cubase not give you the option to transfer all the relative folders and files to save in a new location of your choice. I am aware of setting up the default location, but this is too generic for me. The majority of the time I have no idea what to name my project until AFTER I’ve produced the initial vibe of the beat/song. I don’t like the idea of having to attach a specific name to a generic default location. Having the option to at least do this with the Save As option makes more sense to me as far as structuring and organizing my projects. It appears Cubase ties you to an initial location from the start. Unless I am missing something simple, this does not seem very intuitive. I am also aware that you can back up the song creating a new consolidated project in a new location, but you are still initially forced to save in a generic location first. So my current process in creating new project is creating a new project from a template. Coming up with the production or idea. Saving that project. Then backing up that project to a location that makes sense. Finally going back to erase the original project. That’s a vibe killer in and of itself. Is anyone else dealing with this, or am I simply missing something.
I think “Backup Project” is what you’re looking for. It reorganizes your project into a new folder and copies the selected files over. As @Johnny_Moneto pointed out in a different thread, take care to ensure file dependancies in use by VSTs (e.g. a sampler) are accounted for as the VST doesn’t necessarily tell Cubase the file exists, and it’s not included in the Backup Project processing.
I’d encourage you to read up on Backup Project, but more importantly, test it out yourself so you’ll know when each operation applies to your workflow. Save As is great (for me) when I want to reference a single copy of audio files but use multiple projects, etc. YMMV.
EDIT: I see your reference to “backup up the project makes sense.” I presume there you are referring to the Backup Project operation, so “nevermind.” 
I use exactly the same process as you… possibly with a small adjustment: I do the last step of “cleaning up” when I am on a break or have a slow day. Therefore I never experienced this to kill my vibes.
When working with small project files (<10MB) I don’t even bother with cleaning up more than once per year.
Would be great to have this option as a feature for Save As, to avoid the clean up process altogether.
No, it is not a good idea, and here is why: You might know that all audio files in your current project are only used in this particular project but how is Cubase supposed to know that? And what if you use a wave file from your hard drive in the project, which is also used by some other of your projects?
In order to avoid potentially wrecking other projects Cubase won’t move files, it will only copy them.
Housekeeping is your responsibility as the smart human being that you are.
You have actually stated and reiterated my point exactly. The fact that I indeed know the use and purpose of related files, I am explicitly instructing Cubase to bundle the project and to delete the original location. If a user isn’t aware that the related files are in use by multiple projects then that individual has a lot more issues to be concerned about outside of Cubase, and in life in general for that matter. Besides, it is similar to the same logic involved in removing audio files from your project/audio pool. You get an option to either simply remove the file from your audio pool only or to permanently erase it from the hard drive. Also, when adding files to your project, you get the option to use the files as is from their current location or to copy those files over to a new location. So, in the same fashion it makes perfect sense to have this same logic built into Save As. For example, Save As → Move Or Copy Files? → Delete Source Files?. Again, this action is deliberately explicit, so one can only assume the user’s intent and responsibility involved. It streamlines and removes the janky three step process of 1) saving an initial project in a generic location, 2) backing up the project, 3) then to only go back and manually delete the original location.
I have Cubase’s Preferences set such that any audio files added to the project are copied to the Project folder.
Since Cubase seems to use relative paths instead of absolute, I can rename Project folders any time I like. I can also shunt the Project folder where ever I want and when opening the project, Cubase still finds the files.
Concerning files shared among different projects - some of those files may be used in software other than Cubase: video editing software, for example.