Beginning with 2012SP1, we have the ability to add a CAS to an autonomous primary site. It could be interesting to reverse the proposition by having the ability to remove a CAS above a Primary when a CAS is no longer needed or has been set for a wrong reason.
I know that it could be done through creating another hierarchy and using migration tasks by this is quite difficult for it requires additional hardware.

Current architecture around SCCM’s management of SQL configuration and maintenance is old and hard to use. It requires a lot of manual oversight, and manual SQL tasks. And the default SQL settings created by SCCM are non-optimal. SQL is a powerful beast. Rethink ways SCCM can use it better, and keep it more optimally tuned and configured. Rethink how to run maintenance and backup tasks without downtime or impact to the production sites and deployments (this especially becomes more important with features like Conditional Access, that can never really have downtime.)

It's a real pain to have to tear down and rebuild the MP replicas every time I want to install a servicing update. It would be great to have the update process automatically save the replica state, point the MPs at the primary DB, tear down the MP replicas, do the update and then put it all back.

Configuration Manager currently installs binaries and configures the SQL backup site component service on the database server, running under LocalSystem authority. Many environments have separate groups that host and manage the SQL Server enterprise environment, and do not allow for services or additional software to be installed on them, creating unnecessary conflict and drama when SCCM needs to be installed. SQL Server is a networked service, there shouldn't be a reason to install software on the database server running under a privileged account in order to leverage backup routines.

Support ConfigMgr to be installed on Azure VM IaaS using SQL Paas as DB.

Have the ability to add a second Primary Site Server to an environment running as a standalone site to allow migration from an older Operating System to the latest version e.g. Migrate your 2012 R2 SCCM server from 2008 R2 to 2012 R2 by adding a second primary site server, and allowing settings, data etc. to synchronise. Then retire the old 2008 R2 server.

Service accounts should be domain aware so that they do not attempt to authenticate against the wrong domain to lock out service accounts with the same username but on another domain.

CM12 is able to migrate only one secondary at a time.

Setting up and managing the certificates for MPs, DPs and boot media is not straight forward. Could you improve the certificate management process to reduce the complexity and overhead in managing it. So automation with internal CAs for automatic certificate issuing would be good.

When going through the process of changing the configuration for the site database (in order to move it to a new SQL server), if you are keeping your SQL server name the same, the wizard will not allow you to input the same SQL server name as the old. We want to get rid of our SQL 2008 R2 servers running on Windows 2008 R2 and replace with Server 2016 and SQL 2016, but also keep the same hostname for the new server. Our only option since the wizard doesn't support this scenario is to do a backup and restore.

I found some customers which has "SMS" as name of SCCM site. This make a lot of problems with normal management. This name should also be make as do not allowed (wizard blocks also other names). And if already named, it should allow one time change.

If prerequisite checker fails with a warning there should be an option to continue with the upgrade anyway.