Media Library Enhancement

The Problem and current state of Media Library.
WordPress has become a platform for multiple media types. Sometimes these media file size can exceed what the WordPress up-loader will allow unless someone modifies variables in the back end of the server. (PHP ini variables usually) The easiest method is to upload the file by FTP and then attempt to code in a link. There was an add-on that let you import files but it just basically pretended to upload them and now you have multiple instances of the files. You can let your files be organized by day, year, month automatically or just have all the files dumped into one folder. For some people, managing the files on the server by using FTP to set apart things like audio files, picture files, video files, etc into separate folders makes them easier to keep track of. There are a number of plugins that allow you to virtually organize your media but if you have multiple people adding content, it can still become unruly. This is made worse by all the files being dumped into the same folder structure. WordPress can separate posts out by category, post type and even taxonomy but yet there is no availability to have a better structure for organization.
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How I would like to see things.
Media is stored in the uploads directory first by user name, then by how the admin has set the site up. Either all in one directory or by year only, year, date, month, etc. Admins can add any folder or file that has been added manually to the uploads folder to the media library. They can also set folders for media types for WordPress to automatically put files of a certain type into that folder.
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Why?
I maintain a site that gets an FTP upload of files that are on the small side 75MB up to 200MB on the large side. This is usually several files a day. The files are added to specific directories because of a custom archive system that can display different content based on the directories that those files are uploaded to. I could go into all the details but lets just leave it at this is the only way that our archives can be done at this time. I would love to be able to have those same files available in the media library without duplicating those files in two places and still have my custom folders. Also, having the ability to have a more comprehensive folder organization on the server can also lead to a better way to organize the media library and make control and neat freaks happy the world over.
In short, I think it’s about time that the media library got some love and for the WordPress teams to really take a look at how media on WordPress sites has changed.
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Secondary note:
Please add the ability to completely disable the mediaelement audio/video enhancements to the core. It doesn’t work nearly as good as some other pure HTML5 (no flash) and no matter how I’ve tried to disable it in various themes, it still interferes with my own custom audio.