Since nobody replied, I give you my own experience:
German route hands down.
For the following reasons:
1) Toll/Péages/Maut: via France: 2 x 35 € (one way), via Germany: 2 x 0 €*
* Provided you already have the Swiss vignette autoroutière, which is the case since you live in Pays-de-Gex which should have been part of canton GE in a perfect world.
A40 is one of the most expensive autoroutes in France (cost/km) between Viry toll plaza (gare de péage de Viry) and Bourg-Tossiat.
2) A31 between Toul and F/L border is a freeway and also one of the crappiest autoroutes in France. Whenever a French autoroute is a freeway (autoroute non concédée), expect poor amenities, dirty bathrooms, congestions/pollutions, bad pavement... This is also true for Italy (freeway vs. turnpike).
3) Wallonia has some of the bumpiest autoroutes I have ever seen.
Okay, not like this or this but pretty much like this . Best way to test your shock absorbers or piss off your sleeping kids...
4) German Raststätte are usually cheaper than French aires de service.
5) Beautiful Rhine river scenery
Via France: avoid A6 (Macon-Beaune), use the newer and less congested A39 instead.
Via Germany: avoid A3, A67 and A5 north of Heidelberg .
From Basel Weil, keep driving north on A5, take A6 at Walldorf jct (A5 exit #40) and head towards Mannheim* and immediately after 5 km take A61 (A6 Exit #30) and head towards Koblenz/RP. That way you bypass most German congestions... Keep driving on A61 till you reach the D-NL border and follow signs to Eindhoven / Utrecht / Amsterdam.
* Make sure you don't take A6 towards Heilbronn
ENJOY YOUR TRIP and tell us which route you finally took