Do whatever you preffer. Mini USB is still used alot, so cables will be readily available for quite some time.
Also, mini USB connectors have more 'body', allowing for ~2mm protruding through the wall or frontpanel of a housing. Standard Micro USB sockets are less suitable for that.
btw According the wikipedia article, Mini USB B is not deprecated, only the Mini USB A variant (for USB Host/OTG).