I don't know of any options to set up separate slow query logs per user, but many of the log query parsers can be configured to just print for a user, or exclude a user.

https://code.google.com/p/mysql-log-filter/ for example offers the following ways.

-T=min_query_time
-R=min_rows_examined

-ih, --include-host
-eh, --exclude-host
-iu, --include-user
-eu, --exclude-user
-iq, --include-query