I have used both, in fact I have a current subscription for both. KVS is a standalone tool (the web companion interface isn't comfortable to use, therefore I don't count it), while expertflyer is entirely web-based.
In my eyes there's both good and bad to that - KVS requires updates from time to time and you have to install on your computer (may not be that easy on a business laptop), but it offers more flexibility in terms of sorting results etc. as it is a regular windows (other OS available, I think) application. A disadvantage of KVS (which to other people may be an advantage!) is that it has more options and you need to know what you are doing - i.e. pick between, Sabre, Amadeus etc. and also pick the country you're searching from.
Expertflyer is purely a web interface and thus never requires updates. Also, it is easier to use if you don't the previously described options. Then again it comes with the inflexibility web forms bring with them.

Personally I would say KVS is more for the pro who wants to look behind everything, while expertflyer suits the advanced flyer who wants to see fare classes, find upgrades etc. Of course, someone else might see that differently.