Please allow javascript customization and css branding/theming in the new document library experience. A custom cross-site navigation is one example that is used by many customers. Also many customers want their intranet branded in a different color but office ui fabric blue.
JSLink is also used very often. And don't Forget about all the third-party forms solution provider like Nintex and others.
The new experience provides many advantages, but without customizations it is just not usable for larger intranets anymore.

The sync limit does not match OneDrive for Business, and adds complexity to the end user experience, administration and architecture of SharePoint. Please remove this sync limit.

Currently the new document library experience does not support Managed Navigation. It would be great to have this as currently using the structured navigation seems buggy in the new experience. Specifically, it ignores the "hidden" attribute of structured navigation which can make for some large menus. We love the new experience and are hoping to train users up and roll it out however we need to get navigation right before we can do this.

Upload via Drag&Drop is very easy but it is hard to set the metadata this way.
you need 3 clicks - no user does this much work to set metadata

Number 1 limitation is the fact that we cannot share folders without requiring users to sign-in. Adoption of this product will be limited without this feature.

I contacted support and currently only way to download folder is using IE and open the folder inside Explorer.

Support for other browsers would be great. Alternative is to compress content of folder to ZIP and download that file, like it's available in Microsoft Account version of OneDrive.

We have top bar navigation to our sites. We need to keep this (not having Togo through "Sites")

Make it easier to move documents between folders. It is now possible to use drag & drop to move to sub folders but there are no easy way to move documents up in the structure.

The breadcrumb becomes fairly useless after you have arrived at Document Library level. Folders are still a very important way for users to organize documents. Once you start going into folders, there is no telling from the navigation controls where you are.
This could easily be fixed with an improved breadcrumb which shows the path down to the folder level.

Ideally this should even be an option that you can control from navigation settings, which currently allow zero control over the breadcrumb control.
This is something you should be able to manipulate through configuration without the need for custom code.

Please continue to add the "Open with Explorer" option in the new documents library view

Please make this feature available for SharePoint Online.

"For SharePoint Online, the Opening or downloading documents, viewing items in lists, or viewing item properties event is not available."

https://support.office.com/en-us/article/Configure-audit-settings-for-a-site-collection-a9920c97-38c0-44f2-8bcb-4cf1e2ae22d2?CTT=1&CorrelationId=da58a595-60b0-4710-a856-e43640f776f1&ui=en-US&rs=en-US&ad=US

Now we're trying the display list using new experience which released recently.
One important missing function is there is no way to do customization UI by using JavaScript. As you know the classic (current) experiense have JSLink. Hope to provide it on the new experience, too.

Allow users to complete required metadata when uploading documents using the modern library view. Currently, users are not prompted to complete required fields or select a content type. As a result, the file is left in a checked-out state unless the user knows to edit the properties as a second step after uploading. This breaks sites that have structured metadata and/or specific content type usage requirements. SharePoint has always prompted for these required fields in the past, why remove that functionality?

SharePoint supports dragging files from your desktop into a SharePoint document library, but as soon as you want to drag in a folder containing multiple files/sub-folders this is not supported. You have to recreate the folders manually in document library and then drag in files separately, this consumes a lot of time.

The 'Navigate Up' button on the library ribbon tab is too hidden for users and it also requires an extra click every time you need to go up. The breadcrumb also requires an extra click because you have to click the 'Browse' tab in the ribbon to see it every time.

When using the "Copy" function in a library, it seems the intention is to create a copy of the document in another library.

But when users want to just create a copy of a document in the same location with a different file name, SharePoint throws an error.

Why can the copy function not simply allow a new copy in the same library with a different filename?

In document libraries and in the List View it would be great if the column widths and text size could be adjustable. This would make larger lists a bit more readable to the user rather that letting Sharepoint decide the column width.

give an easy way for users to copy a file from a SharePoint site document library into their own OneDrive For Business. It was announced at the "FutureOfSharePoint" webinar that users will be able to copy a file from their OneDrive to a SharePoint site and I think it would also be beneficial to allow users to copy files the other way. I
m hoping this is already planned but just not mentioned.