MySQL can take more than an hour to start
The solution is to drastically decrease the number of files.  I see 3 approaches, depending on your version:

Plan A (the only option for 5.6 and earlier):

Set innodb_file_per_table=OFF, restart your client, then do ALTER TABLE ... ENGINE=InnoDB all but the 1000 largest tables.  This will shovel all the non-huge tables into ibdata1.

Plan B (if you have at least 5.7, and you have 10-1000 databases):

If you have multiple databases, create a General Tablespace per database.  Put non-huge tables into those tablespaces.

Leave the huge tables in their own tablespaces.

To facilitate either Plan A or B, write a SELECT against information_schema that creates the desired ALTER statements, then execute them.

Plan C:  Move to 8.0, which might actually work reasonably fast with a million tables due to its Data Dictionary.  (Or, you might need a combo of Plan C together with A or B.)