cannot set default frequency or mode

I see your point, but don't currently see an easy solution. Ubuntu CPU governor is usually "performance", when the system boots for maximum speed during bootup. After 60 seconds (reasonably chosen boot time) the system explicitly switches the governor to "ondemand".

There is a small conflict here — if indicator-cpufreq chooses some frequency after you log in, Ubuntu system scripts may override it just a bit later, because of the above hardcoded behaviour, which is actually okay for many users. Thoughts?

Well how does the system switch it from "performance" to "ondemand"?
Isn't there a way to run a script after 70 seconds that would change the value in to the prefered one then? Like the system does.

Yep, it's possible to either edit the script in /etc/init.d/ondemand (line 27) and replace "ondemand" with a preferred governor. Or keep a similar command sequence in /etc/rc.local.

Well, if you have a SSD, Ubuntu boots in less than 10 seconds (about 7) to the desktop.
Because of that I lowered the time from 60 seconds to 10.
Thanks for the hint.