I noticed that SD generated FPL's through Slovenian airspace will never be accepted because SD uses 'coordinates' rather than official entry/exit points. (I had one unaltered SD generated plan rejected recently for this reason). Slovenian AIP:

REF AIP SLOVENIA ENR 1.10 PARA 1.3. B. SPECIALARANGEMENTS FOR IFR AND VFR FLIGHTS (ICAO NOTIFICATION OF DIFFERENCE) FLIGHTPLANS WITH FLIGHT ROUTES CROSSING FIR LJLA BOUNDARY OR VOLUMES OF CONTROLAIRSPACE SHALL INCLUDE OFFICIALLY PUBLISHED ENTRY/EXIT REPORTING POINTS.COORDINATES OR ANY OTHER NAMES ARE NOT ALLOWED THEREFORE SUCH FPL WILL BEREJECTED.

.. not sure what we can do about that in SD. I guess we have to remember to make manual changes to the plans.

It is not correct to say that coordinates are not accepted in practice in VFR flight plans. I use unaltered FPL's from SD to travel between Germany and France all the time and the FPL's have always been accepted so far.