It would be nice if I could FTP a .bak file to my webroot or /data/ folder and do a restore on the database from that location.

FTP is better at session management for large transfers than HTTP is and this will avoid customer timeout issues restoring databases.

I'd actually love to see a backup system with self-managed restores available

It would be great to allow you to rename a cloud site. It would also be great to make a copy of an existing site into a new (or existing) site. For example to make a QA/test link from an existing production site, or be able to go the other way as needed as well.

When administering my web page and database, I have questions about various elements of the UI (such as what "Memory usage" really means, and why it resets after a period of time). Unfortunately, I don't see any links on screen to refer to documentation for the various pages.

IP based SSL instead of SNI SSL for older devices

A "scale by metric" option which auto-scales the site according to CPU usage.

Be able to move a domain from one CloudSite to another.

Show the IP address you need to change in DNS not only under domains, but also under CloudSites so it's easier to find. The shared IP, separate from the dedicated.