I didn't get the part about "Having filter set is not resolving the issue, since optimized, but still slow queries are not logged", but I agree with the point about log_slow_filter being an empty string. The parameter description in Percona says:
"If the string is empty, then the filter is disabled"
http://www.percona.com/doc/percona-server/5.1/diagnostics/slow_extended.html?id=percona-server:features:slow_extended_51&redirect=2

In Percona server it is indeed so, but in MariaDB, if the parameter is empty, no slow logging is performed – see the test case added to the description.
To make SELECT SLEEP appear in the slow log, log_slow_filter has to be set to something containing 'query_cache_miss'.

Not reproducible on maria/5.3.

From MariaDB documentation:

"Multiple options are separated by ','. If you don't specify any options (default) everything will be logged."

Once we switched to mariadb, log_slow_filter was set to be empty (to log all slow queries), but we noticed no queries in slow log.

https://kb.askmonty.org/en/slow-query-log-extended-statistics/

log_slow_filter

You can define which queries to log to the slow query log by setting the variable log_slow_filter to a combination of the following values:

admin
Log adminstrative statements (create, optimize, drop etc...)
filesort
Log statement if it uses filesort
filesort_on_disk
Log statement if it uses filesort that needs temporary tables on disk
full_join
Log statements that doesn't uses indexes to join tables
full_scan
Log statements that uses full table scans
query_cache
Log statements that are resolved by the query cache
query_cache_miss
Log statements that are not resolved by the query cache
tmp_table
Log statements that uses in memory temporary tables
tmp_table_on_disk
Log statements that uses temporary tables on disk
Multiple options are separated by ','. If you don't specify any options (default) everything will be logged.

Looks like documentation has been adjusted

Still, this sentence doesn't seem to be correct
" The default value is ' ', to be compatible with MySQL 5.1. "
First, the default value is actually a list of all available options.
Second, if it's doesn't work in the same fashion as 5.1 then it's not compatible at all!

The problem with the empty value is fixed in 5.5.31. The default value in 5.5 remains the full list of values, so I updated the text in the following way:

was:
Multiple options are separated by ','. If you don't specify any options (default) everything will be logged.

now:
Multiple options are separated by ','. If you don't specify any options everything will be logged.

The text quoted in the previous comment ("The default value is ' ', to be compatible with MySQL 5.1") relates to log_slow_verbosity (not to log_slow_filter) and remains true.

I have updated https://mariadb.com/kb/en/slow-query-log-extended-statistics/ to include all log_slow_query options