Create slave site takes time because JMS generate PHP code that by normal processing.
The PHP code that is generated is to speed-up the switch decisions.
When you have a very large number of website (> 1,000 websites) there are some specific setting to use the "letter tree" present in JMS and that can be configured in the "multisites.cfg.php" file.
If the JMS Template rule that you are using to create the slave site has a rule that can allow retreiving a slave site based on the URL, it is possible to develop a specific code to speed-up the processing to retreive a slave site.
This can reduce the time to compute the "master index" PHP code and to take the switch decision.
This can only be done with specific development as the JMS template rule should be computed with specific code to replace the rule.
Create the "master index" require to recompute all the websites information and the time increase with the number of website.
The only solution is a specific development that can replace the computation of the index by a specific PHP code developemnt that simulate the same result as your JMS Template rule.
If you want that we develop such specific code, this is possible with our billable support that can be ordered at
www.jms2win.com/en/joomla-multisite?page...35&category_id=1