To customize the format of time and date displayed on the top panel indicator, and set a different format than any other locale format, you'll have to edit manually from dconf Editor.
Open dconf Editor:
Navigate to com > canonical > indicator > datetime
1. Set "time-format" to "custom"
2. Set "custom-time-format" to the format you want.
3. Make sure that "show-clock" is check-marked.
To check out available formatting options, see the manpage of strftime.
~$ man strftime
My setting is %Y-%m-%d %H:%M:%S
Which looks like this: 2015-01-09 09:04:51
My other favorite setting is %Y.%m.%d. %a. %H:%M:%S
Which looks like this: 2015.07.02. cs. 09:04:51 (where cs. is the local abbreviation of Thursday)
With the custom date-time format you can still use the options for the calendar (show-calendar, etc.), but the options for the clock will make no change on the displayed custom time-date format.